8TOP

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide

PDB DOI: https://doi.org/10.2210/pdb8TOP/pdb
EM Map EMD-41459: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-03 Released: 2024-08-07
Deposition Author(s): Zhou, T., Morano, N.C., Roark, R.S., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.52 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide

Wang, H.

To be published.

Macromolecule Content

Total Structure Weight: 744.59 kDa
Atom Count: 38,845
Modelled Residue Count: 4,755
Deposited Residue Count: 6,510
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505 DS-SOSIP gp120	A [auth O] C [auth Q] E [auth S] S [auth A] U [auth C] A [auth O], C [auth Q], E [auth S], S [auth A], U [auth C], W [auth E]	481	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A [auth O] Focus chain C [auth Q] Focus chain E [auth S] Focus chain S [auth A] Focus chain U [auth C] Focus chain W [auth E]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505 DS-SOSIP glycoprotein gp41	B [auth P] D [auth R] F [auth T] T [auth B] V [auth D] B [auth P], D [auth R], F [auth T], T [auth B], V [auth D], X [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth R] Focus chain F [auth T] Focus chain V [auth D] Focus chain X [auth F]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of antibody GPZ6-b.01	G [auth H] H [auth J] K [auth M] M [auth U] O [auth W] G [auth H], H [auth J], K [auth M], M [auth U], O [auth W], Q [auth Y]	237	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of antibody GPZ6-b.01	I [auth K] J [auth L] L [auth N] N [auth V] P [auth X] I [auth K], J [auth L], L [auth N], N [auth V], P [auth X], R [auth Z]	214	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], CA [auth c], EA [auth e], GA [auth g], HA [auth h], AA [auth a], CA [auth c], EA [auth e], GA [auth g], HA [auth h], JA [auth j], KA [auth k], MA [auth m], Y [auth G]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain Y [auth G]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], DA [auth d], FA [auth f], IA [auth i], LA [auth l], BA [auth b], DA [auth d], FA [auth f], IA [auth i], LA [auth l], Z [auth I]	4		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain LA [auth l] Focus chain Z [auth I] Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain LA [auth l] Focus chain Z [auth I]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth Q] SDF format, chain AC [auth S] SDF format, chain AD [auth C] SDF format, chain BB [auth Q] SDF format, chain BC [auth T] SDF format, chain BD [auth C] SDF format, chain CB [auth Q] SDF format, chain CC [auth A] SDF format, chain CD [auth D] SDF format, chain DB [auth Q] SDF format, chain DC [auth A] SDF format, chain DD [auth D] SDF format, chain EB [auth Q] SDF format, chain EC [auth A] SDF format, chain ED [auth E] SDF format, chain FB [auth Q] SDF format, chain FC [auth A] SDF format, chain FD [auth E] SDF format, chain GB [auth Q] SDF format, chain GC [auth A] SDF format, chain GD [auth E] SDF format, chain HB [auth Q] SDF format, chain HC [auth A] SDF format, chain HD [auth E] SDF format, chain IB [auth Q] SDF format, chain IC [auth A] SDF format, chain ID [auth E] SDF format, chain JB [auth Q] SDF format, chain JC [auth A] SDF format, chain JD [auth E] SDF format, chain KB [auth Q] SDF format, chain KC [auth A] SDF format, chain KD [auth E] SDF format, chain LB [auth Q] SDF format, chain LC [auth A] SDF format, chain LD [auth E] SDF format, chain MB [auth Q] SDF format, chain MC [auth A] SDF format, chain MD [auth E] SDF format, chain NA [auth O] SDF format, chain NB [auth R] SDF format, chain NC [auth A] SDF format, chain ND [auth E] SDF format, chain OA [auth O] SDF format, chain OB [auth R] SDF format, chain OC [auth A] SDF format, chain OD [auth E] SDF format, chain PA [auth O] SDF format, chain PB [auth S] SDF format, chain PC [auth A] SDF format, chain PD [auth E] SDF format, chain QA [auth O] SDF format, chain QB [auth S] SDF format, chain QC [auth C] SDF format, chain QD [auth F] SDF format, chain RA [auth O] SDF format, chain RB [auth S] SDF format, chain RC [auth C] SDF format, chain SA [auth O] SDF format, chain SB [auth S] SDF format, chain SC [auth C] SDF format, chain TA [auth O] SDF format, chain TB [auth S] SDF format, chain TC [auth C] SDF format, chain UA [auth O] SDF format, chain UB [auth S] SDF format, chain UC [auth C] SDF format, chain VA [auth O] SDF format, chain VB [auth S] SDF format, chain VC [auth C] SDF format, chain WA [auth O] SDF format, chain WB [auth S] SDF format, chain WC [auth C] SDF format, chain XA [auth O] SDF format, chain XB [auth S] SDF format, chain XC [auth C] SDF format, chain YA [auth O] SDF format, chain YB [auth S] SDF format, chain YC [auth C] SDF format, chain ZA [auth Q] SDF format, chain ZB [auth S] SDF format, chain ZC [auth C] MOL2 format, chain AB [auth Q] MOL2 format, chain AC [auth S] MOL2 format, chain AD [auth C] MOL2 format, chain BB [auth Q] MOL2 format, chain BC [auth T] MOL2 format, chain BD [auth C] MOL2 format, chain CB [auth Q] MOL2 format, chain CC [auth A] MOL2 format, chain CD [auth D] MOL2 format, chain DB [auth Q] MOL2 format, chain DC [auth A] MOL2 format, chain DD [auth D] MOL2 format, chain EB [auth Q] MOL2 format, chain EC [auth A] MOL2 format, chain ED [auth E] MOL2 format, chain FB [auth Q] MOL2 format, chain FC [auth A] MOL2 format, chain FD [auth E] MOL2 format, chain GB [auth Q] MOL2 format, chain GC [auth A] MOL2 format, chain GD [auth E] MOL2 format, chain HB [auth Q] MOL2 format, chain HC [auth A] MOL2 format, chain HD [auth E] MOL2 format, chain IB [auth Q] MOL2 format, chain IC [auth A] MOL2 format, chain ID [auth E] MOL2 format, chain JB [auth Q] MOL2 format, chain JC [auth A] MOL2 format, chain JD [auth E] MOL2 format, chain KB [auth Q] MOL2 format, chain KC [auth A] MOL2 format, chain KD [auth E] MOL2 format, chain LB [auth Q] MOL2 format, chain LC [auth A] MOL2 format, chain LD [auth E] MOL2 format, chain MB [auth Q] MOL2 format, chain MC [auth A] MOL2 format, chain MD [auth E] MOL2 format, chain NA [auth O] MOL2 format, chain NB [auth R] MOL2 format, chain NC [auth A] MOL2 format, chain ND [auth E] MOL2 format, chain OA [auth O] MOL2 format, chain OB [auth R] MOL2 format, chain OC [auth A] MOL2 format, chain OD [auth E] MOL2 format, chain PA [auth O] MOL2 format, chain PB [auth S] MOL2 format, chain PC [auth A] MOL2 format, chain PD [auth E] MOL2 format, chain QA [auth O] MOL2 format, chain QB [auth S] MOL2 format, chain QC [auth C] MOL2 format, chain QD [auth F] MOL2 format, chain RA [auth O] MOL2 format, chain RB [auth S] MOL2 format, chain RC [auth C] MOL2 format, chain SA [auth O] MOL2 format, chain SB [auth S] MOL2 format, chain SC [auth C] MOL2 format, chain TA [auth O] MOL2 format, chain TB [auth S] MOL2 format, chain TC [auth C] MOL2 format, chain UA [auth O] MOL2 format, chain UB [auth S] MOL2 format, chain UC [auth C] MOL2 format, chain VA [auth O] MOL2 format, chain VB [auth S] MOL2 format, chain VC [auth C] MOL2 format, chain WA [auth O] MOL2 format, chain WB [auth S] MOL2 format, chain WC [auth C] MOL2 format, chain XA [auth O] MOL2 format, chain XB [auth S] MOL2 format, chain XC [auth C] MOL2 format, chain YA [auth O] MOL2 format, chain YB [auth S] MOL2 format, chain YC [auth C] MOL2 format, chain ZA [auth Q] MOL2 format, chain ZB [auth S] MOL2 format, chain ZC [auth C]	AB [auth Q] AC [auth S] AD [auth C] BB [auth Q] BC [auth T] AB [auth Q], AC [auth S], AD [auth C], BB [auth Q], BC [auth T], BD [auth C], CB [auth Q], CC [auth A], CD [auth D], DB [auth Q], DC [auth A], DD [auth D], EB [auth Q], EC [auth A], ED [auth E], FB [auth Q], FC [auth A], FD [auth E], GB [auth Q], GC [auth A], GD [auth E], HB [auth Q], HC [auth A], HD [auth E], IB [auth Q], IC [auth A], ID [auth E], JB [auth Q], JC [auth A], JD [auth E], KB [auth Q], KC [auth A], KD [auth E], LB [auth Q], LC [auth A], LD [auth E], MB [auth Q], MC [auth A], MD [auth E], NA [auth O], NB [auth R], NC [auth A], ND [auth E], OA [auth O], OB [auth R], OC [auth A], OD [auth E], PA [auth O], PB [auth S], PC [auth A], PD [auth E], QA [auth O], QB [auth S], QC [auth C], QD [auth F], RA [auth O], RB [auth S], RC [auth C], SA [auth O], SB [auth S], SC [auth C], TA [auth O], TB [auth S], TC [auth C], UA [auth O], UB [auth S], UC [auth C], VA [auth O], VB [auth S], VC [auth C], WA [auth O], WB [auth S], WC [auth C], XA [auth O], XB [auth S], XC [auth C], YA [auth O], YB [auth S], YC [auth C], ZA [auth Q], ZB [auth S], ZC [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth Q] Focus chain AC [auth S] Focus chain AD [auth C] Focus chain BB [auth Q] Focus chain BC [auth T] Focus chain BD [auth C] Focus chain CB [auth Q] Focus chain CC [auth A] Focus chain CD [auth D] Focus chain DB [auth Q] Focus chain DC [auth A] Focus chain DD [auth D] Focus chain EB [auth Q] Focus chain EC [auth A] Focus chain ED [auth E] Focus chain FB [auth Q] Focus chain FC [auth A] Focus chain FD [auth E] Focus chain GB [auth Q] Focus chain GC [auth A] Focus chain GD [auth E] Focus chain HB [auth Q] Focus chain HC [auth A] Focus chain HD [auth E] Focus chain IB [auth Q] Focus chain IC [auth A] Focus chain ID [auth E] Focus chain JB [auth Q] Focus chain JC [auth A] Focus chain JD [auth E] Focus chain KB [auth Q] Focus chain KC [auth A] Focus chain KD [auth E] Focus chain LB [auth Q] Focus chain LC [auth A] Focus chain LD [auth E] Focus chain MB [auth Q] Focus chain MC [auth A] Focus chain MD [auth E] Focus chain NA [auth O] Focus chain NB [auth R] Focus chain NC [auth A] Focus chain ND [auth E] Focus chain OA [auth O] Focus chain OB [auth R] Focus chain OC [auth A] Focus chain OD [auth E] Focus chain PA [auth O] Focus chain PB [auth S] Focus chain PC [auth A] Focus chain PD [auth E] Focus chain QA [auth O] Focus chain QB [auth S] Focus chain QC [auth C] Focus chain QD [auth F] Focus chain RA [auth O] Focus chain RB [auth S] Focus chain RC [auth C] Focus chain SA [auth O] Focus chain SB [auth S] Focus chain SC [auth C] Focus chain TA [auth O] Focus chain TB [auth S] Focus chain TC [auth C] Focus chain UA [auth O] Focus chain UB [auth S] Focus chain UC [auth C] Focus chain VA [auth O] Focus chain VB [auth S] Focus chain VC [auth C] Focus chain WA [auth O] Focus chain WB [auth S] Focus chain WC [auth C] Focus chain XA [auth O] Focus chain XB [auth S] Focus chain XC [auth C] Focus chain YA [auth O] Focus chain YB [auth S] Focus chain YC [auth C] Focus chain ZA [auth Q] Focus chain ZB [auth S] Focus chain ZC [auth C] Interactions & Density Focus chain AB [auth Q] Focus chain AC [auth S] Focus chain AD [auth C] Focus chain BB [auth Q] Focus chain BC [auth T] Focus chain BD [auth C] Focus chain CB [auth Q] Focus chain CC [auth A] Focus chain CD [auth D] Focus chain DB [auth Q] Focus chain DC [auth A] Focus chain DD [auth D] Focus chain EB [auth Q] Focus chain EC [auth A] Focus chain ED [auth E] Focus chain FB [auth Q] Focus chain FC [auth A] Focus chain FD [auth E] Focus chain GB [auth Q] Focus chain GC [auth A] Focus chain GD [auth E] Focus chain HB [auth Q] Focus chain HC [auth A] Focus chain HD [auth E] Focus chain IB [auth Q] Focus chain IC [auth A] Focus chain ID [auth E] Focus chain JB [auth Q] Focus chain JC [auth A] Focus chain JD [auth E] Focus chain KB [auth Q] Focus chain KC [auth A] Focus chain KD [auth E] Focus chain LB [auth Q] Focus chain LC [auth A] Focus chain LD [auth E] Focus chain MB [auth Q] Focus chain MC [auth A] Focus chain MD [auth E] Focus chain NA [auth O] Focus chain NB [auth R] Focus chain NC [auth A] Focus chain ND [auth E] Focus chain OA [auth O] Focus chain OB [auth R] Focus chain OC [auth A] Focus chain OD [auth E] Focus chain PA [auth O] Focus chain PB [auth S] Focus chain PC [auth A] Focus chain PD [auth E] Focus chain QA [auth O] Focus chain QB [auth S] Focus chain QC [auth C] Focus chain QD [auth F] Focus chain RA [auth O] Focus chain RB [auth S] Focus chain RC [auth C] Focus chain SA [auth O] Focus chain SB [auth S] Focus chain SC [auth C] Focus chain TA [auth O] Focus chain TB [auth S] Focus chain TC [auth C] Focus chain UA [auth O] Focus chain UB [auth S] Focus chain UC [auth C] Focus chain VA [auth O] Focus chain VB [auth S] Focus chain VC [auth C] Focus chain WA [auth O] Focus chain WB [auth S] Focus chain WC [auth C] Focus chain XA [auth O] Focus chain XB [auth S] Focus chain XC [auth C] Focus chain YA [auth O] Focus chain YB [auth S] Focus chain YC [auth C] Focus chain ZA [auth Q] Focus chain ZB [auth S] Focus chain ZC [auth C]