Molecular Visualization Resourses

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Deep View Swiss-Pdb Viewer.  This program allows alignments to be made between different proteins.

Nucleic Acid Structure Files

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Index of Structures

A RNA Structures

ARNA Idealized full turn duplex structure produced by Hyperchem for every possible unique dinucleotide stack.

---12345678901

5'-TACGCATCCTT-3'

3'-AAGGATGCGTA-5'

ARN035 X-ray crystal structure of an RNA duplex

---12345678901234

5'-UUAUAUAUAUAUAA-3'

3'-AATAUAUAUAUAUU-5'

---87654321098765

A.C.Dock-Bregeon, B.Chevrier, A.Podjarny, J.Johnson, J.S.De Bear, G.R.Gough, P.T.Gilham, D.Moras, Crystallographic Structure of an RNA Helix: [U(U-A)6A]2. J.Mol.Biol., 209, 459-474, 1989.

B DNA Structures

BDNA Idealized 11-mer duplex structure produced by Hyperchem for every possible unique dinucleotide stack

---12345678901

5'-TACGCATCCTT

3'-AAGGATGCGTA

BDL001 X-ray crystal structure of the Dickerson Dodecamer

---123456789012

5'-CGCGAATTCGCG-3'

3'-GCGCTTAAGCGC-5'

---432109876543

H.R.Drew, R.M.Wing, T.Takano, C.Broka, S.Tanaka, K.Itakura, R.E.Dickerson, Structure of a B-DNA Dodecamer. Conformation and Dynamics Proc.Natl.Acad.Sci.U.S.A., 78, 2179-2183, 1981.

BDL038 X-ray crystal structure of B DNA showing water of hydration

---123456789012

5'-CGCAAATTTGCG-3'

3'-CGCAAATTTGCG-5'

---432109876543

K.J.Edwards, D.G.Brown, N.Spink, S.Neidle Molecular Structure of the B-DNA Dodecamer d(CGCAAATTTGCG)2; An Examination of Propeller Twist and Minor-Groove Water Structure at 2.2 Angstroms Resolution, J.Mol.Biol., 226, 1161-1173, 1992.

Z DNA Structures

ZDNA Idealized 11-mer structure produced by Hyperchem for every possible unique dinucleotide stack

---12345678901

5'-TACGCATCCTT

3'-AAGGATGCGTA

ZDF002 X-ray crystal structure

---123456

5'-CGCGCG-3'

3'-GCGCGC-5'

---210987

R.V.Gessner, C.A.Frederick, G.J.Quigley, A.Rich, A.H.-J.Wang, The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom Atomic Resolution. Geometry, Conformation, and Ionic Interactions of d(CGCGCG) J.Biol.Chem., 264, 7921-7935, 1989.

Triplex DNA

L.Van Meervelt, D.Vlieghe, A.Dautant, B.Gallois, G.Precigoux, O.Kennard, High-Resolution Structure of a DNA Helix Forming (C.G)*G, Base Triplets Nature, 374, 742-744, 1995.

Intramolecular Triplex DNA

1GN7 K.M.Koshlap,P.Schultze,H.Brunar,P.B.Dervan, J.Feigon

"Solution Structure Of An Intramolecular DNA Triplex Containing An N7-Glycosylated Guanine Which Mimics A Protonated Cytosine" Biochemistry 1997, 36, 2659.

This is an NMR-derived structure of triplex DNA, which contains a modified N7-glycosylated G which is a mimic for a protonated C in a conventional Hoogsteen pyrimidine base pair.

Questions.

a) What is the nature of the base pairing between the strands? Draw the base pair and give its type (Watson-Crick, Hoogsteen, etc).

b) What are the glycosyl bond conformations, syn or anti?

c) What is the direction of each of the three strands (i.e., label the 5' and 3' ends of the strands shown in the schematic, which strands are parallel and antiparallel)?

d) What is the structure of the loops? (Hint: how do the bases stack?)

e) How does the Watson-Crick duplex portion compare in structure to A DNA and B DNA?

f) How does the N-7G-G base pair compare to a C+G or TG Hoogsteen base pair?

Intercalated 4-Stranded DNA

C.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich, Crystal Structure of Intercalated Four-Stranded d(C3T) Proc.Nat.Acad.Sci.U.S.A., 91, 11636-11640, 1994.

UDF027 pending

C.Kang, I.Berger, C.Lockshin, R.Ratliff, R.Moyzis, A.Rich Stable Loop in the Crystal Structure of the Intercalated Four-Stranded Cytosine-Rich Metazoan Telomere Proc.Natl.Acad.Sci.U.S.A., 92, 3874-3878, 1995.

Quadruplex DNA

UDL018

C.Kang, X.Zhang, R.Ratliff, R.Moyzis, A.Rich, Crystal Structure of 4-Stranded Oxytricha Telomeric DNA, Nature, 356, 126-131, 1992.

Bulge Loop DNA

UDM010 Residue 17 is the bulge loop nucleotide

---1234567890 123

5'-CGCAGAATTC GCG-3'

3'-GCG CGGAAGACGC-5'

---654 3210987654

L.Joshua-Tor, F.Frolow, E.Appella, H.Hope, D.Rabinovich, J.L.Sussman The Three-Dimensional Structures of Bulge -Containing DNA Fragments, J.Mol.Biol., 225, 397-431, 1992.

Intercalators

Mono-Intercalators

DRB007 S.C Jain, H.M.Sobell, Visualization of Drug-Nucleic Acid Interactions at Atomic Resolution. VIII. Structures of Two Ethidiumdinucleoside Monophosphate Crystalline Complexes Containing Ethidium: Cytidylyl(3'-5')Guanosine. J.Biomol.Struct.Dyn., 1, 1179-1194, 1984.

This is the structure of ethidium bromide complexed to a self-complementary RNA dinucleotide CpG via intercalation. Ethidium bromide is the most commonly used stain for duplex DNA and has been the subject for many intercalation studies.

5'-C1--G2-3'

EB

3'-G4--G3-5'
 

Daunomycin

DDF018 M.H.Moore, W.N.Hunter, B.Langlois D'Estaintot, O.Kennard, A-Drug Interactions: The Crystal Structure of d(CGATCG) Complexed with Daunomycin J.Mol.Biol., 206, 693-705, 1989.

5'-C1---G2--A3--T4-C5---G6-3'

D14 D13

3'-G12--C11-T10-A9-G8---C7-5'

This is the structure of a commonly used anticancer drug bound to DNA. Daunomycin is composed of an aromatic ring system linked to an amino glycoside sugar ring.
 
 

Nogalamycin

DDF049 C.K.Smith, G.J.Davies, E.J.Dodson, M.H.Moore, A-Nogalamycin Interactions: The Crystal Structure of (TGATCA) Complexed with Nogalamycin, ochemistry, 34, 415-425, 1995.

This is a structure of a self complementary DNA duplex hexamer complexed to two Nogalamycin drugs via intercalation. These drugs are interesting in that they contain bulky groups on either ends, one of which must thread through the helix in order to bind.

5'-T1---G2--A3--T4-C5---A6-3'

N14 N13

3'-A12--C11-T10-A9-G8---T7-5'

Bis-Intercalators

DDD030 Q.Gao, L.D.Williams, M.Egli, D.Rabinovich, S.-L.Chen, G.J.Quigley, A.Rich,Drug-Induced DNA Repair: X-Ray Structure of a DNA-Ditercalinium Complex Proc.Natl.Acad.Sci.U.S.A., 88, 2422-2426, 1991.

This is the structure of a ditercalinium (residue 9) complexed to duplex DNA via bis-intercalation. Ditercalinium is composed of two intercalators covalently linked to each other which binds to DNA according to the nearest neighbor exclusion principle. That is, the geometry of an intercalation site precludes the formation of another intercalation site that makes use of one of its base pairs.

5'-C1-G2-C3-G4-3'

|--9--|

3'-G8-C7-G6-C5-5'
 

Triostin

DDF007 A.H.-J.Wang, G.Ughetto, G.J.Quigley, T.Hakoshima, G.A.Van Der Marel, J.H.Van Boom, A.Rich,The Molecular Structure of a DNA-Triostin a Complex, Science, 225, 1115-1121, 1984.

This is a fascinating structure of a self complementary duplex DNA molecule complexed with another bis-intercalator, the drug triostin. In this case two drugs are complexed to the DNA and each drug induces an alternate form of base pairing between the AT base pairs adajacent to the intercalation sites. The drug is composed of two aromatic rings (residues 13 and 14 on the first drug) attached to a cyclic peptide linker (residues 15-22).

5'-C1--G2--T3--A4--C5--G6-3'

13======14 24======23

3'-G12-C11-A10-T9--G8--C7-5'

MINOR GROOVE BINDERS

Distamycin. The prototypical minor groove binder that was used to first illustrate the concept of affinity cleaving.

2dnd.pdb Single molecule binding mode.

M. Coll, C.A.Frederick,A.H.-J.Wang, A. Rich, "A bifurcated hydrogen-bonded conformation in the d(A•T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin" Proc.Nat.Acad.Sci.USA, 84, 8385 (1987).

Strand A: C1 G2 C3 A4 A5 A6 T7 T8 T9 G10 C11 G12 N9-Distamyc-N1

Strand B: G12 C11 G10 T9 T8 T7 A6 A5 A4 C3 G2 C1
 
 

DMY: DISTAMYCIN

1. The distamycin molecule is identified by the code DMY. Visualize how it binds to the minor groove by viewing in space fill mode and coloring the individual strands and the distamycin.

2. What bases are being recognized by distamycin and how?

304d.pdb (the pdb structure only gives the coordinates for one strand, the ndb gives coordinates for the complete molecule.)
 
 

X.Chen, B.Ramakrishnan, M., Crystal structures of the side-by-side binding of distamycin to at-containing DNA octamers d(ICITACIC) AND d(ICATATIC) J. MOL.BIOL. 267 1157 (1997)
 
 

Strand A and B: 5'-I1 C2 A3 T4 A5 T6 I7 C8-3', where I = inosine

Ligand A and B: DISTAMYCIN A

1. How is the pair of distamycin molecules oriented (parallel or antiparallel)?
2. How does the width of the minor groove compare with the width of B form DNA?
3. What H-bonding interactions take place between the distamycin units and the DNA?

Cis-Platin Adduct (1AIO.pdb)
 Chime File for Cis-Platin
 Chime File for Cis-Platin (Liping Sun '98)

1aio.pdb Crystal structure of a double-stranded DNA containing the major adduct of the anticancer drug cisplatin

(5'-d(*CC(BR)UCT[PT(NH3)2(GGP)]*TCTCC)-3'), (5'-d(*GGAGACCAGAGG)-3')

CHAIN: A, B, C, D;

P.M.Takahara,A.C.Rosenzweig,C.A.Frederick,S.J.Lippard , P.M.Takahara,A.C.Rosenzweig,C.A.Frederick, S.J.Lippard, Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin NATURE 377 649 (1995)
 
 

Crosslinked DNA Structures

1ddp.pdb Solution Structure Of A Cisplatin-Induced [Catagctatg]2 Interstrand Cross-Link

(5'-D(CATAGCTATG)-3')

Chain: A, B;

Heterogen: Cis-Platinum-(NH3)2

Expdta Nmr, 10 Structures

L.Zhu,H.Huang,B.R.Reid,G.P.Drobny,P.B.Hopkins

H.Huang,L.Zhu,B.R.Reid,G.P.Drobny,P.B.Hopkins Solution Structure Of A Cisplatin-Induced DNA Interstrand Cross-Link Science 270 1842 (1995)

 Chime File for Cis-Syn Cyclobutane Dimer

 Chime File for (6-4) and Dewar Products

DNA Bending

1D98 (NDB: BDL006) H.C.M.Nelson, J.T.Finch, B.F.Luisi, A.Klug, The Structure of an Oligo(dA).Oligo(dT) Tract and Its Biological Implications, Nature, 330, 221-226, 1987.

This is a crystal structure of an A6-tract that discovered the presence of bifurcated H-bonds in the A-tract (hydrogen bonding between one H and two acceptors.)

5'-C1--G2--C3--A4--A5--A6--A7--A8--A9--G10-C11-G12-3'

3'-G22-C21-G20-T19-T18-T17-T16-T15-T14-C13-G14-C13-5'

Cap-DNA structure

1CGP (NDB: PDR006), S.C.Schultz, G.C.Shields, T.A.Steitz Crystal Structure of a CAP-DNA Complex: The DNA Is Bent by 90 Degrees Science, 253, 1001-1007, 1991.

This is the structure of a protein-DNA complex with a bend which allowed the direction of an A6-tract bend to be determined unambiguously by the phase sensitive detection methodology. The protein is units 9A-205A and 9B-205B. The DNA chain is 3C-33C and 3D-33D. For the C and D chains:

5'-G3--T4--C5--A6--C7--A8--C9--T10-T11-T12-T13-C14-G15-3'

3'-T33-A32-T31-A30-C29-A28-G27-T26-G25-T24-G23-A22-A21-A20-A19-G18-C17-G16-5'

Protein-DNA Interactions

Helix-turn-helix motif.

A. Mondragon, S. C. Harrison, The Phage 434 Cro/OR1 Complex at 2.5 Angstroms Resolution, J.Mol.Biol. 219, 321-334 (1991).

Chain A 20 nt:

5-A1 A2 G3 T4 A5 C6 A7 A8 A9 C10 T11 T12 T13 C14 T15 T16 G17 T18 A19 T20-3

3-T40C39A38T37G36T35T34T33G32 A31 A30 A29 G28 A27 A26 C25 A24 T23 A22 T21-5

Chain B 20 nt (complementary strand)

Chain L (Left operator) 71 aa (residues 41-111, but 107-111 not visible)
 

Chain R 71aa (Right operator repressor): same sequence, residues 112-175 visible.

Leucine Zipper Motif.

T.E.Ellenberger, C.J.Brandl, K.Struhl, S.C.Harrison, The GCN4 Basic Region Leucine Zipper Binds DNA as a Dimer of Uninterrupted Alpha Helices: Crystal Structure of the Protein-DNA Complex, Cell, 71, 1223-1237 (1992).

Chain A 20 nt:

5'-T T C C T A T G A C T C A A T C C A G T T-3'

3'- A G G A T A C T G A G T T A G G T C A A A-5'

Chain B 20 nt: (complementary strand)

Chain C 57 aa (41-97, methionine not visible):
 

Chain D 57 aa: (same sequence, residues 98-154)
 

Zinc Finger Motif. Zif268

NDB file: PDT006, PDB file: 1ZAA

N.P.Pavletich, C.O.Pabo, Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 Angstroms, Science 252 809-817 (1991).

Chain A 11nt:

5'-A G C G T G G G C G T-3'

3'- C G C A C C C G C A T-5'

Chain B 11 nt: complementary strand

Chain C 87aa: (only residues 25- visible)
 

Chain D: 3 Zn atoms: 201, 202, 203

Beta-Strand Motif

Pdb file: 1CMA A dimer of dimers that recognizes two met boxes ((AGACGTCT).

W.S.Somers,S.E.V.Phillips, Crystal structure of the met repressor-operator complex at 2.8 angstroms resolution reveals DNA recognition by beta-strands. Nature359, 387 (1992)

J.B.Rafferty,W.S.Somers,I.Saint-Girons, S.E.V.Phillips, Three dimensional crystal structures of E. coli met repressor with and without corepressor Nature341 705 (1989).

Chains A&B: (one dimeric pair binding to one half of the operator). Residues 21-29 consitute the -strand which forms an antiparallel -sheet that binds to the major groove and recognizes one half of the operator sequence.
 

One half of pallindromic 19-mer sequence (-1 to 17)

C T1 T A G A C G T C T

D A19 G A C G T C T A

SAM A 105 27 S-ADENOSYLMETHIONINE

SAM B 105 27 S-ADENOSYLMETHIONINE

Restriction/Modification Enzymes

Restriction Enzyme

Methylation Modification
HaeIII Methylase (Khahani, '98)

RNA Polymerase

Ribosome

Reference. "Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue," Biochemistry, 24 2058 (1985)

Protein. 124 Amino acids.

Substrate. Uridine vanadate, UVC

1. Select all and view as backbone.

2. Select UVC and view as sticks.

3. Select His 119 and His 12 and Lys 41 as ball and stick.

4tna_pb = 1TN1.pdb + 4tna.pdb. X-ray crystal structure of yeast tRNAphe superimposed with coordinates of Pb ions which give insight into the mechanism of site-specific tRNA cleavage catalyzed by lead ion.

References:

R. S. Brown, J. C. Dewan, A. Klug "Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA, Biochemistry 24, 4785 (1985)

R. S. Brown, B. E. Hingerty, J. C. Dewan, A. Klug Pb(II)-catalysed cleavage of the sugar-phosphate backbone of yeast tRNAphe - Implications for lead toxicity and self-splicing RNA", Nature 303, 543 (1983).

Pb(1) is bound in the T-psi-C loop (U59, C60). Pb(2) is bound in the extra loop region. Pb(3) is bound in the anticodon loop. The coordination sites for the Pb ions could not be fully characterized because of difficulties in assigning bound water ligands at 3.0 angstroms resolution. A description of the interaction regions is given in reference 1 above. The quantity provided in the occupancy field represents the electron count. At present the coordinates for the pH 7.4 Pb-tRNA are not available. Thus only the coordinates for the pb ions are included in this entry. Refinement of the pH 5.0 and pH 7.4 structures indicated that they changed very little from the native structure. The only real difference is the presence of the Pb ions. Also, in the pH 7.4 structure, the sugar-phosphate backbone is cleaved between residues D 17 (5,6-dihydrouridine) and G 18.

Ribozyme Structures

Reference: T.Tuschl,C.Gohlke,T.M.Jovin,E.Westhof,F.Eckstein, "A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements, Science 266,785- (1994).

UHX026 Hammerhead ribozyme structure (pending)

H.W.Pley, K.M.Flaherty, D.B.Mckay Three-Dimensional Structure of a Hammerhead Ribozyme, Nature, 372, 68-74, 1994.

AminoAcyl tRNA synthetase
 Chime Script for aa tRNA synthetase (Duan, '98)