5U1F | pdb_00005u1f

Initial contact of HIV-1 Env with CD4: Cryo-EM structure of BG505 DS-SOSIP trimer in complex with CD4 and antibody PGT145


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth M]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054493 3000071 SCOP2B (2022-06-29)
I [auth M]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054739 3000071 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
D [auth B]SCOP2B SuperfamilyVirus ectodomain 8085614 3001628 SCOP2B (2022-06-29)
C [auth A]SCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
B [auth D]SCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)
A [auth C]SCOP2B Superfamilygp120 core 8080371 3001390 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth M]MCM_Ne5u1fM1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
H [auth L]MCM_Ne5u1fL1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
G [auth H]MCM_Ne5u1fH1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
FMCM_Ne5u1fF1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
EMCM_Ne5u1fE1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
D [auth B]MCM_Ne5u1fB1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
C [auth A]MCM_Ne5u1fA1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
B [auth D]MCM_Ne5u1fD1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)
A [auth C]MCM_Ne5u1fC1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Osmotin-likeT: CARF (CRISPR-associated Rossmann fold) domainsF: MCM_NECOD (develop294)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
I [auth M]T-cell surface glycoprotein CD4 1V-1C-1V-1C-LIKE Homo sapiens (human) CD4 V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE RPI 1V-1C-1V-1C-LIKE IMGT (202610-0)
H [auth L]Fab PGT145 L-KAPPA Homo sapiens (human) IGKV2-28*01, IGKV2D-28*01, IGKJ1*01, IGKC*01 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202610-0)
G [auth H]Fab PGT145 VH-CH1 Homo sapiens (human) IGHV1-8*03, IGHJ1*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05, IGHG1*12, IGHG1*14, IGHG1*13, IGHG1*09, IGHG1*10, IGHG1*07, IGHG1*11 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
H [auth L]Light ChainIGKV2 Kappabg505 ds-sosip gp120 | bg505 ds-sosip gp120 | bg505 ds-sosip gp120SAbDab (2026-03-20)
G [auth H]Heavy ChainIGHV1 -bg505 ds-sosip gp120 | bg505 ds-sosip gp120 | bg505 ds-sosip gp120SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth M]PF05790Immunoglobulin C2-set domain (C2-set)Immunoglobulin C2-set domainDomain
I [auth M]PF00047Immunoglobulin domain (ig)Immunoglobulin domainMembers of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.
Domain
I [auth M]PF09191CD4, extracellular (CD4-extracel)CD4, extracellularMembers of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histo ...Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth M]T-cell surface glycoprotein CD4
H [auth L]PGT145 light chain---
G [auth H]PGT145 heavy chain---
D [auth B],
E,
F
BG505 SOSIP gp41
A [auth C],
B [auth D],
C [auth A]
BG505 DS-SOSIP gp120

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
I [auth M]PharosP01730

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
G [auth H]TYS Parent Component: TYR

RESIDAA0172

PSI-MOD :  O4'-sulfo-L-tyrosine MOD:00181