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Viral protein PDB id
2znf
Jmol
Contents
Protein chain
18 a.a.
Metals
_ZN
PDB id:
2znf
Name: Viral protein
Title: High-resolution structure of an HIV zinc fingerlike domain via a new nmr-based distance geometry approach
Structure: Gag polyprotein. Chain: a. Engineered: yes
Source: Human immunodeficiency virus 1. Organism_taxid: 11676
NMR struc: 16 models
Authors: M.F.Summers,T.L.South,B.Kim,D.R.Hare
Key ref:
M.F.Summers et al. (1990). High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach. Biochemistry, 29, 329-340. PubMed id: 2105740 DOI: 10.1021/bi00454a005
Date:
30-Mar-90     Release date:   15-Oct-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q70622  (GAG_HV1LW) -  Gag polyprotein
Seq:
Struc: 		500 a.a.
18 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  

 

 
DOI no: 10.1021/bi00454a005 Biochemistry 29:329-340 (1990)
PubMed id: 2105740  
 
 
High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach.
M.F.Summers, T.L.South, B.Kim, D.R.Hare.
 
  ABSTRACT  
 
A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the "goodness" of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significantly different from that of a "classical" DNA-binding zinc finger. Residues C(1)-F(2)-N(3)-C(4)-G(5)-K(6) fold in a manner virtually identical with the folding observed by X-ray crystallography for related residues in the iron domain of rubredoxin; superposition of all main-chain and Cys side-chain atoms of residues C(1)-K(6) of Zn(p55F1) onto residues C(6)-Y(11) and C(39)-V(44) of rubredoxin gives RMSDs of 0.46 and 0.35 A, respectively. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20026680 A.M.Fuller, E.G.Cook, K.J.Kelley, and M.L.Pardue (2010).
Gag proteins of Drosophila telomeric retrotransposons: collaborative targeting to chromosome ends.
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Crystal structure of zinc-finger domain of Nanos and its functional implications.
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PDB code: 3alr
18668206 J.J.Kuszewski, R.A.Thottungal, G.M.Clore, and C.D.Schwieters (2008).
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.
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17610897 B.M.Lee, B.A.Buck-Koehntop, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2007).
Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.
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PDB code: 2jox
17070546 J.Zhou, R.L.Bean, V.M.Vogt, and M.Summers (2007).
Solution structure of the Rous sarcoma virus nucleocapsid protein: muPsi RNA packaging signal complex.
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PDB code: 2ihx
16425239 B.Zagrovic, and W.F.van Gunsteren (2006).
Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
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15790571 E.Kellenberger, C.Dominguez, S.Fribourg, E.Wasielewski, D.Moras, A.Poterszman, R.Boelens, and B.Kieffer (2005).
Solution structure of the C-terminal domain of TFIIH P44 subunit reveals a novel type of C4C4 ring domain involved in protein-protein interactions.
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PDB code: 1z60
16064056 V.D'Souza, and M.F.Summers (2005).
How retroviruses select their genomes.
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15271979 S.L.Heilman-Miller, T.Wu, and J.G.Levin (2004).
Alteration of nucleic acid structure and stability modulates the efficiency of minus-strand transfer mediated by the HIV-1 nucleocapsid protein.
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12525635 E.G.Lee, A.Alidina, C.May, and M.L.Linial (2003).
Importance of basic residues in binding of rous sarcoma virus nucleocapsid to the RNA packaging signal.
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12783894 M.J.Heath, S.S.Derebail, R.J.Gorelick, and J.J.DeStefano (2003).
Differing roles of the N- and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing.
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12639244 M.L.Schito, A.Goel, Y.Song, J.K.Inman, R.J.Fattah, W.G.Rice, J.A.Turpin, A.Sher, and E.Appella (2003).
In vivo antiviral activity of novel human immunodeficiency virus type 1 nucleocapsid p7 zinc finger inhibitors in a transgenic murine model.
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12736264 R.J.Simpson, E.D.Cram, R.Czolij, J.M.Matthews, M.Crossley, and J.P.Mackay (2003).
CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
  J Biol Chem, 278, 28011-28018.
PDB code: 1p7a
12743295 S.Rashkova, A.Athanasiadis, and M.L.Pardue (2003).
Intracellular targeting of Gag proteins of the Drosophila telomeric retrotransposons.
  J Virol, 77, 6376-6384.  
11932404 J.Guo, T.Wu, B.F.Kane, D.G.Johnson, L.E.Henderson, R.J.Gorelick, and J.G.Levin (2002).
Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein.
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11980477 S.Cho, and D.W.Hoffman (2002).
Structure of the beta subunit of translation initiation factor 2 from the archaeon Methanococcus jannaschii: a representative of the eIF2beta/eIF5 family of proteins.
  Biochemistry, 41, 5730-5742.
PDB codes: 1k81 1k8b
11891280 S.Rashkova, S.E.Karam, and M.L.Pardue (2002).
Element-specific localization of Drosophila retrotransposon Gag proteins occurs in both nucleus and cytoplasm.
  Proc Natl Acad Sci U S A, 99, 3621-3626.  
11554444 D.E.Wilcox, A.D.Schenk, B.M.Feldman, and Y.Xu (2001).
Oxidation of zinc-binding cysteine residues in transcription factor proteins.
  Antioxid Redox Signal, 3, 549-564.  
11700292 E.M.Ostertag, and H.H.Kazazian (2001).
Biology of mammalian L1 retrotransposons.
  Annu Rev Genet, 35, 501-538.  
10677209 D.J.Klein, P.E.Johnson, E.S.Zollars, R.N.De Guzman, and M.F.Summers (2000).
The NMR structure of the nucleocapsid protein from the mouse mammary tumor virus reveals unusual folding of the C-terminal zinc knuckle.
  Biochemistry, 39, 1604-1612.
PDB codes: 1dsq 1dsv
  11045620 H.T.Chen, P.Legault, J.Glushka, J.G.Omichinski, and R.A.Scott (2000).
Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription.
  Protein Sci, 9, 1743-1752.
PDB code: 1dl6
9888182 E.Lehmann, R.Zenobi, and S.Vetter (1999).
Matrix-assisted laser desorption/ionization mass spectra reflect solution-phase zinc finger peptide complexation.
  J Am Soc Mass Spectrom, 10, 27-34.  
9922156 E.N.Chertova, B.P.Kane, C.McGrath, D.G.Johnson, R.C.Sowder, L.O.Arthur, and L.E.Henderson (1998).
Probing the topography of HIV-1 nucleocapsid protein with the alkylating agent N-ethylmaleimide.
  Biochemistry, 37, 17890-17897.  
9478919 E.Remy, H.de Rocquigny, P.Petitjean, D.Muriaux, V.Theilleux, J.Paoletti, and B.P.Roques (1998).
The annealing of tRNA3Lys to human immunodeficiency virus type 1 primer binding site is critically dependent on the NCp7 zinc fingers structure.
  J Biol Chem, 273, 4819-4822.  
9520442 O.N.Danilevskaya, C.Tan, J.Wong, M.Alibhai, and M.L.Pardue (1998).
Unusual features of the Drosophila melanogaster telomere transposable element HeT-A are conserved in Drosophila yakuba telomere elements.
  Proc Natl Acad Sci U S A, 95, 3770-3775.  
9430589 R.N.De Guzman, Z.R.Wu, C.C.Stalling, L.Pappalardo, P.N.Borer, and M.F.Summers (1998).
Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.
  Science, 279, 384-388.
PDB code: 1a1t
  9827993 Y.Gao, K.Kaluarachchi, and D.P.Giedroc (1998).
Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.
  Protein Sci, 7, 2265-2280.
PDB code: 1cl4
9922136 Y.Kodera, K.Sato, T.Tsukahara, H.Komatsu, T.Maeda, and T.Kohno (1998).
High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
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PDB code: 1nc8
9218433 D.S.Sem, D.R.Casimiro, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1997).
NMR spectroscopic studies of the DNA-binding domain of the monomer-binding nuclear orphan receptor, human estrogen related receptor-2. The carboxyl-terminal extension to the zinc-finger region is unstructured in the free form of the protein.
  J Biol Chem, 272, 18038-18043.  
8841116 A.Hammarström, K.D.Berndt, R.Sillard, K.Adermann, and G.Otting (1996).
Solution structure of a naturally-occurring zinc-peptide complex demonstrates that the N-terminal zinc-binding module of the Lasp-1 LIM domain is an independent folding unit.
  Biochemistry, 35, 12723-12732.
PDB code: 1zfo
  8551614 E.Schmalzbauer, B.Strack, J.Dannull, S.Guehmann, and K.Moelling (1996).
Mutations of basic amino acids of NCp7 of human immunodeficiency virus type 1 affect RNA binding in vitro.
  J Virol, 70, 771-777.  
8836095 I.Jones, and D.Stuart (1996).
Journey to the core of HIV.
  Nat Struct Biol, 3, 818-820.  
8995054 M.L.Pardue, O.N.Danilevskaya, K.Lowenhaupt, J.Wong, and K.Erby (1996).
The gag coding region of the Drosophila telomeric retrotransposon, HeT-A, has an internal frame shift and a length polymorphic region.
  J Mol Evol, 43, 572-583.  
8620007 S.P.Lee, and M.K.Han (1996).
Zinc stimulates Mg2+-dependent 3'-processing activity of human immunodeficiency virus type 1 integrase in vitro.
  Biochemistry, 35, 3837-3844.  
8665919 Z.Kuklenyik, S.Yao, and L.G.Marzilli (1996).
Similar conformations of hairpins with TTT and TTTT sequences: NMR and molecular modeling evidence for T.T base pairs in the TTTT hairpin.
  Eur J Biochem, 236, 960-969.  
  7579651 D.Barrick (1995).
Depletion and replacement of protein metal ligands.
  Curr Opin Biotechnol, 6, 411-418.  
8597114 R.Kaptein, M.Slijper, and R.Boelens (1995).
Structure and dynamics of the lac repressor-operator complex as determined by NMR.
  Toxicol Lett, 82, 591-599.  
7545668 Y.Tzfati, H.Abeliovich, D.Avrahami, and J.Shlomai (1995).
Universal minicircle sequence binding protein, a CCHC-type zinc finger protein that binds the universal minicircle sequence of trypanosomatids. Purification and characterization.
  J Biol Chem, 270, 21339-21345.  
7664053 G.C.Pérez-Alvarado, C.Miles, J.W.Michelsen, H.A.Louis, D.R.Winge, M.C.Beckerle, and M.F.Summers (1994).
Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP.
  Nat Struct Biol, 1, 388-398.
PDB code: 1ctl
7664042 J.W.Schwabe, and A.Klug (1994).
Zinc mining for protein domains.
  Nat Struct Biol, 1, 345-349.  
7925381 M.S.Lee, D.S.Sem, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
  Eur J Biochem, 224, 639-650.  
  8039495 P.A.Tucker, D.Tsernoglou, A.D.Tucker, F.E.Coenjaerts, H.Leenders, and P.C.van der Vliet (1994).
Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding.
  EMBO J, 13, 2994-3002.
PDB code: 1adt
8210313 A.T.Brünger, and M.Nilges (1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
  Q Rev Biophys, 26, 49.  
  8350412 C.B.Jonsson, and M.J.Roth (1993).
Role of the His-Cys finger of Moloney murine leukemia virus integrase protein in integration and disintegration.
  J Virol, 67, 5562-5571.  
8233798 F.M.Taylor, and D.W.Martindale (1993).
Retroviral-type zinc fingers and glycine-rich repeats in a protein encoded by cnjB, a Tetrahymena gene active during meiosis.
  Nucleic Acids Res, 21, 4610-4614.  
8460131 J.A.Landro, and P.Schimmel (1993).
Metal-binding site in a class I tRNA synthetase localized to a cysteine cluster inserted into nucleotide-binding fold.
  Proc Natl Acad Sci U S A, 90, 2261-2265.  
  8480366 K.Riehemann, and C.Sorg (1993).
Sequence homologies between four cytoskeleton-associated proteins.
  Trends Biochem Sci, 18, 82-83.  
8506369 K.Sakaguchi, N.Zambrano, E.T.Baldwin, B.A.Shapiro, J.W.Erickson, J.G.Omichinski, G.M.Clore, A.M.Gronenborn, and E.Appella (1993).
Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein.
  Proc Natl Acad Sci U S A, 90, 5219-5223.  
  8318898 M.J.Sutcliffe (1993).
Representing an ensemble of NMR-derived protein structures by a single structure.
  Protein Sci, 2, 936-944.  
8272423 M.W.MacArthur, and J.M.Thornton (1993).
Conformational analysis of protein structures derived from NMR data.
  Proteins, 17, 232-251.  
  8230441 R.D.Berkowitz, J.Luban, and S.P.Goff (1993).
Specific binding of human immunodeficiency virus type 1 gag polyprotein and nucleocapsid protein to viral RNAs detected by RNA mobility shift assays.
  J Virol, 67, 7190-7200.  
  8510214 R.J.Gorelick, D.J.Chabot, A.Rein, L.E.Henderson, and L.O.Arthur (1993).
The two zinc fingers in the human immunodeficiency virus type 1 nucleocapsid protein are not functionally equivalent.
  J Virol, 67, 4027-4036.  
8435043 S.Ayehunie, B.Johansson, A.Sönnerborg, D.W.Zewdie, S.Britton, and O.Strannegård (1993).
Sequence analysis of selected regions of the env (V3 loop and gp41) and gag (p7) reading frames of Ethiopian human immunodeficiency virus type 1 strains.
  Arch Virol, 128, 229-239.  
  8443588 T.L.South, and M.F.Summers (1993).
Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC.
  Protein Sci, 2, 3.
PDB codes: 1hvn 1hvo
8274645 Y.Mély, E.Piémont, M.Sorinas-Jimeno, H.de Rocquigny, N.Jullian, N.Morellet, B.P.Roques, and D.Gérard (1993).
Structural and dynamic characterization of the aromatic amino acids of the human immunodeficiency virus type I nucleocapsid protein zinc fingers and their involvement in heterologous tRNA(Phe) binding: a steady-state and time-resolved fluorescence study.
  Biophys J, 65, 1513-1522.  
  1397325 A.Surovoy, D.Waidelich, and G.Jung (1992).
Nucleocapsid protein of HIV-1 and its Zn2+ complex formation analysis with electrospray mass spectrometry.
  FEBS Lett, 311, 259-262.  
  1280325 J.G.Kim, and L.D.Hudson (1992).
Novel member of the zinc finger superfamily: A C2-HC finger that recognizes a glia-specific gene.
  Mol Cell Biol, 12, 5632-5639.  
  1731111 J.W.Bess, P.J.Powell, H.J.Issaq, L.J.Schumack, M.K.Grimes, L.E.Henderson, and L.O.Arthur (1992).
Tightly bound zinc in human immunodeficiency virus type 1, human T-cell leukemia virus type I, and other retroviruses.
  J Virol, 66, 840-847.  
  1304355 M.F.Summers, L.E.Henderson, M.R.Chance, J.W.Bess, T.L.South, P.R.Blake, I.Sagi, G.Perez-Alvarado, R.C.Sowder, and D.R.Hare (1992).
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.
  Protein Sci, 1, 563-574.
PDB code: 1aaf
1422154 M.L.Donlan, F.K.Brown, and P.W.Jeffs (1992).
Solution conformation of human big endothelin-1.
  J Biomol NMR, 2, 407-420.  
1332027 M.R.Chance, I.Sagi, M.D.Wirt, S.M.Frisbie, E.Scheuring, E.Chen, J.W.Bess, L.E.Henderson, L.O.Arthur, and T.L.South (1992).
Extended x-ray absorption fine structure studies of a retrovirus: equine infectious anemia virus cysteine arrays are coordinated to zinc.
  Proc Natl Acad Sci U S A, 89, 10041-10045.  
  1639074 N.Morellet, N.Jullian, H.De Rocquigny, B.Maigret, J.L.Darlix, and B.P.Roques (1992).
Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR.
  EMBO J, 11, 3059-3065.  
1449599 P.F.Agris, R.H.Guenther, H.Sierzputowska-Gracz, L.Easter, W.Smith, C.C.Hardin, T.A.Santa-Coloma, J.W.Crabb, and L.E.Reichert (1992).
Solution structure of a synthetic peptide corresponding to a receptor binding region of FSH (hFSH-beta 33-53).
  J Protein Chem, 11, 495-507.  
  1303769 P.R.Blake, J.B.Park, Z.H.Zhou, D.R.Hare, M.W.Adams, and M.F.Summers (1992).
Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.
  Protein Sci, 1, 1508-1521.
PDB code: 1zrp
1422151 R.Pachter, C.H.Arrowsmith, and O.Jardetzky (1992).
The effect of selective deuteration on magnetization transfer in larger proteins.
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1472657 W.H.Graham, E.S.Carter, and R.P.Hicks (1992).
Conformational analysis of Met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multidimensional NMR and molecular modeling.
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1379318 W.T.Miller, and P.Schimmel (1992).
A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product.
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A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognition.
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1850126 E.Khan, J.P.Mack, R.A.Katz, J.Kulkosky, and A.M.Skalka (1991).
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Metal-binding sites in proteins.
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  1959614 J.G.Omichinski, G.M.Clore, K.Sakaguchi, E.Appella, and A.M.Gronenborn (1991).
Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy.
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PDB code: 1ncp
2005183 M.F.Summers (1991).
Zinc finger motif for single-stranded nucleic acids? Investigations by nuclear magnetic resonance.
  J Cell Biochem, 45, 41-48.  
  1367670 W.J.Chazin (1991).
New nuclear magnetic resonance structures and structural methodology.
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1912345 Y.Mely, F.Cornille, M.C.Fournié-Zaluski, J.L.Darlix, B.P.Roques, and D.Gérard (1991).
Investigation of zinc-binding affinities of Moloney murine leukemia virus nucleocapsid protein and its related zinc finger and modified peptides.
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2385599 L.M.Green, and J.M.Berg (1990).
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  2168981 P.Dupraz, S.Oertle, C.Meric, P.Damay, and P.F.Spahr (1990).
Point mutations in the proximal Cys-His box of Rous sarcoma virus nucleocapsid protein.
  J Virol, 64, 4978-4987.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.