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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE IN A HELICAL CONFORMATION
 
Authors :  N. I. Nicely, S. M. Dennison, G. Kelsoe, H. -X. Liao, S. M. Alam, B. F. Hayn
Date :  22 Apr 10  (Deposition) - 17 Nov 10  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,P
Biol. Unit 1:  A,B,P  (1x)
Biol. Unit 2:  A,B,P  (2x)
Keywords :  Hiv-1, Hiv Gp41, Mper, 13H11, 2F5, Z13, 4E10, Fab Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. I. Nicely, S. M. Dennison, G. Kelsoe, Y. Ueda, H. X. Liao, S. M. Alam, B. F. Haynes
Crystal Structure Of A Non-Neutralizing Hiv-1 Gp41 Envelope Antibody Demonstrates Neutralization Mechanism Of Gp41 Antibodies
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GP41
    ChainsP
    EngineeredYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    Other DetailsCHEMICALLY SYNTHESIZED PEPTIDE OF SEQUENCE DERIVED FROM THE MEMBRANE PROXIMAL EXTERNAL REGION OF GP41
    SyntheticYES
 
Molecule 2 - ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T CELL
    Expression System CommonHUMAN
    Expression System OrganKIDNEY
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentMOUSE FV,HUMAN FC
    Organism CommonMOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090, 9606
 
Molecule 3 - ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T CELL
    Expression System CommonHUMAN
    Expression System OrganKIDNEY
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentMOUSE FV,HUMAN FC
    Organism CommonMOUSE, HUMAN
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090, 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABP
Biological Unit 1 (1x)ABP
Biological Unit 2 (2x)ABP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NH21Mod. Amino AcidAMINO GROUP
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NH22Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:83 , ASN B:84 , GLU B:85 , HOH B:306BINDING SITE FOR RESIDUE EDO B 231

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Ala B:125 -Pro B:126
5Phe B:148 -Pro B:149
6Glu B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MNW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MNW)

(-) Exons   (0, 0)

(no "Exon" information available for 3MNW)

(-) 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 A from PDB  Type:PROTEIN  Length:216
 aligned with Q8TCD0_HUMAN | Q8TCD0 from UniProtKB/TrEMBL  Length:239

    Alignment length:218
                                                             53                                                                                                                                                                                       
                                                           52 |                                                                                                                                                                                       
                                    29        39        49  | |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        
         Q8TCD0_HUMAN    20 GDVVMTQSPLSLPVTLGQPASISCRSTQSLVYS-DGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKITRVEAEDVGVYFCMQGTHWPSTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 236
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee--...eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnw A   0 LDIQLTQSPSSLAM--GQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFASIRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 211
                                     9   |  | 19        29 |||||| 33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
                                        13 16            30A|||||                                                                                                                                                                                     
                                                          30B||||                                                                                                                                                                                     
                                                           30C|||                                                                                                                                                                                     
                                                            30D||                                                                                                                                                                                     
                                                             30E|                                                                                                                                                                                     
                                                              30F                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with S6B291_HUMAN | S6B291 from UniProtKB/TrEMBL  Length:466

    Alignment length:217
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
         S6B291_HUMAN    20 EVQLLESGGDLVQPGGSLRLSCAASGFTFSTYAMSWVRQAPGKGLEWVSGIGDSGHSIYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCATGSQWPGDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 236
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.--..eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..----.ee...eeeee........eeeee..-------.eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnw B   1 QIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQV--KGLKWMGWINTETGEPTYADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGW----LHWGLGTTLTVSSASTKGPSVFPLAP-------GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 225
                                    10        20        30        40  |     50  |     59        69        79   |||  86        96    |  106       116       126       138       148     ||163     ||174     ||185       195    |||208       218       
                                                                  40 43       52A                            82A||            96  101                      126     136               154|||    169|      180|               200||                    
                                                                                                              82B|                                                                    156||     171       182                203|                    
                                                                                                               82C                                                                     157|                                   205                    
                                                                                                                                                                                        162                                                          

Chain P from PDB  Type:PROTEIN  Length:20
 aligned with ENV_HV1BR | P03377 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:20
                                   667       677
            ENV_HV1BR   658 QEKNEQELLELDKWASLWNW 677
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 3mnw P 653 QEKNEQELLELDKWASLWNx 672
                                   662       672
                                             672-NH2

   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  (0, 0)

(no "SCOP Domain" information available for 3MNW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MNW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MNW)

(-) Gene Ontology  (21, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8TCD0_HUMAN | Q8TCD0)

Chain B   (S6B291_HUMAN | S6B291)

Chain P   (ENV_HV1BR | P03377)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1BR | P033771env 1erf 1fav 1p5a 1u6u 1u6v 2zzo 3g9r 3vgx 3vtp
        Q8TCD0_HUMAN | Q8TCD01hzh 1n0x 3mnv 3mnz 3pgf 4d9q 4nug 4nuj 4nwt 5viy 5vj6 5vod
        S6B291_HUMAN | S6B2913mnz 4eow 5c7k 5cus 5d9q 5veb 5vic 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        Q8TCD0_HUMAN | Q8TCD03cfj 3cfk 4nwu
        S6B291_HUMAN | S6B2914llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

3mnv CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
3mnz CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE BEARING ALA SUBSTITUTIONS IN A HELICAL CONFORMATION
3mo1 CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
3moa CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 17 AA GP41 MPER-DERIVED PEPTIDE
3mob CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 11 AA GP41 MPER-DERIVED PEPTIDE
3mod CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED IGG) WITH 11 AA GP41 MPER-DERIVED PEPTIDE