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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 NEUTRALIZING HUMAN FAB 4E10 IN COMPLEX WITH A 13-RESIDUE PEPTIDE CONTAINING THE 4E10 EPITOPE ON GP41
 
Authors :  R. M. F. Cardoso, M. B. Zwick, R. L. Stanfield, R. Kunert, J. M. Binley, H. D. R. Burton, I. A. Wilson
Date :  09 Jul 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Biol. Unit 3:  H (1x),I (1x),L (1x),M (1x),P (1x),Q (1x)
Keywords :  Antibody-Epitope Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. F. Cardoso, M. B. Zwick, R. L. Stanfield, R. Kunert, J. M. Binley, H. Katinger, D. R. Burton, I. A. Wilson
Broadly Neutralizing Anti-Hiv Antibody 4E10 Recognizes A Helical Conformation Of A Highly Conserved Fusion-Associate Motif In Gp41
Immunity V. 22 163 2005
PubMed-ID: 15723805  |  Reference-DOI: 10.1016/J.IMMUNI.2004.12.011

(-) Compounds

Molecule 1 - FAB 4E10
    Chains: L, M
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: OVARY
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: LIGHT CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 4E10
    Chains: H, I
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: OVARY
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: HEAVY CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENVELOPE POLYPROTEIN GP160
    Chains: P, Q
    Engineered: YES
    Fragment: TRANSMEMBRANE GLYCOPROTEIN
    Synonym: GP41
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HILMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  I M Q
Biological Unit 3 (1x): H (1x)I (1x)L (1x)M (1x)P (1x)Q (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:174 , PRO H:175 , VAL H:177 , SER H:186 , LEU H:187 , SER H:188 , SER L:162 , SER L:176 , SER L:177 , THR L:178 , HOH L:774BINDING SITE FOR RESIDUE GOL L 701
2AC2SOFTWAREGLY H:164 , ARG L:61 , GLU L:81 , HOH L:770 , HOH L:813BINDING SITE FOR RESIDUE GOL L 702
3AC3SOFTWAREPRO H:214 , PRO L:8 , GLY L:9 , THR L:10 , HOH L:761BINDING SITE FOR RESIDUE GOL L 703

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3I:22 -I:92
4I:142 -I:208
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Ser M:7 -Pro M:8
6Tyr M:140 -Pro M:141
7Phe I:148 -Pro I:149
8Glu I:150 -Pro I:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TZG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TZG)

(-) Exons   (0, 0)

(no "Exon" information available for 1TZG)

(-) Sequences/Alignments

Asymmetric 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 H from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains d1tzgh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                 d1tzgh2 H:114-232 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                           SCOP domains
               CATH domains 1tzgH01 H:1-109 Immunoglobulins                                                                                            1tzgH02 H:110-232 Immunoglobulins                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1tzg H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK  232
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||  230  
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|       
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225       
                                                                                                               82C                 100C||||||                                                    157|                                   205                         
                                                                                                                                    100D|||||                                                     162                                                               
                                                                                                                                     100E||||                                                                                                                       
                                                                                                                                      100F|||                                                                                                                       
                                                                                                                                       100G||                                                                                                                       
                                                                                                                                        100H|                                                                                                                       
                                                                                                                                         100I                                                                                                                       


Chain I from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains d1tzgi1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                                 d1tzgi2 I:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1tzgI01 I:1-109 Immunoglobulins                                                                                            1tzgI02 I:110-228 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1tzg I    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||   
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|   
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225   
                                                                                                               82C                 100C||||||                                                    157|                                   205                     
                                                                                                                                    100D|||||                                                     162                                                           
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1tzgl1 L:1-106 automated matches                                                                          d1tzgl2 L:107-213 automated matches                                                                         SCOP domains
               CATH domains 1tzgL01 L:1-108 Immunoglobulins                                                                              1tzgL02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1tzg L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A                                                                                                                                                                                          


Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1tzgm1 M:1-106 automated matches                                                                          d1tzgm2 M:107-213 automated matches                                                                         SCOP domains
               CATH domains 1tzgM01 M:1-108 Immunoglobulins                                                                              1tzgM02 M:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1tzg M    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A                                                                                                                                                                                          


Chain P from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                1tzg P  669 GWNWFDITNWGK  680
                                   678  


Chain Q from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                1tzg Q  669 GWNWFDITNWGK  680
                                   678
   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  (4, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1tzgL02L:109-211
1b1tzgL01L:1-108
1c1tzgM01M:1-108
1d1tzgI02I:110-228
1e1tzgH02H:110-232
1f1tzgH01H:1-109
1g1tzgI01I:1-109
1h1tzgM02M:109-211

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TZG)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1TZG)

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