Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN EOD-GT6 IN COMPLEX WITH A PUTATIVE VRC01 GERMLINE PRECURSOR FAB
 
Authors :  J. -P. Julien, J. Jardine, W. R. Schief, I. A. Wilson
Date :  19 Mar 13  (Deposition) - 10 Apr 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Hiv-1 Gp120, Cd4 Binding, Vrc01-Like Broadly Neutralizing Antibodies, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jardine, J. P. Julien, S. Menis, T. Ota, O. Kalyuzhniy, A. Mcguire, D. Sok, P. S. Huang, S. Macpherson, M. Jones, T. Nieusma, J. Mathison, D. Baker, A. B. Ward, D. R. Burton, L. Stamatatos, D. Nemazee, I. A. Wilson, W. R. Schief
Rational Hiv Immunogen Design To Target Specific Germline B Cell Receptors.
Science V. 340 711 2013
PubMed-ID: 23539181  |  Reference-DOI: 10.1126/SCIENCE.1234150

(-) Compounds

Molecule 1 - PUTATIVE VRC01 GERMLINE PRECURSOR FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PUTATIVE VRC01 GERMLINE PRECURSOR FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN, EOD-GT6
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , NAG A:202 , HOH A:343BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWAREHIS A:14 , SER A:16 , SER A:17 , ASN A:65 , NAG A:201BINDING SITE FOR RESIDUE NAG A 202

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:7 -A:158
2A:15 -A:151
3A:51 -A:88
4A:99 -A:105
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:136 -L:196

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:142 -Pro L:143
5Arg A:8 -Pro A:9
6Asp A:33 -Glu A:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JPK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JPK)

(-) Exons   (0, 0)

(no "Exon" information available for 4JPK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee...hhhhhhhh..........eee.........eee..........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee......hhhhhheeeee..eeeee.hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpk A    1 DTITLPCRPAPPPHCSSNITGLILTRDGGVSNDETEIFRPSGGDMRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLATSVEIACTGAGHCAISRAKWANTLKQIASKLREQFGARTIIFKQSSGGDPEFVTHSFNCGGEFFYCDSTQLFASTWF  169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpk H    1 QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGKNSDYNWDFQHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212 
                                                                              52A                            82A||               100A|||                                                                                                                 
                                                                                                              82B|                100B||                                                                                                                 
                                                                                                               82C                 100C|                                                                                                                 
                                                                                                                                    100D                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d4jpkl1 L:1-109 automated matches                                                                      d4jpkl2 L:110-214 automated matches                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jpk L    1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQYEFFGQGTKLEIKRSTVAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  214
                                    10        20        30        40        50        60        70        80        90||     106       116       126       136       146       156       166       176       186       196       206        
                                                                                                                     91|    103|                                                                                                            
                                                                                                                      96     106
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JPK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JPK)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:8 - Pro A:9   [ RasMol ]  
    Asp A:33 - Glu A:34   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:142 - Pro L:143   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4jpk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ENV_HV1H2 | P04578
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ENV_HV1H2 | P04578
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08

(-) Related Entries Specified in the PDB File

4jpi 4jpj