8TOX

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

PDB DOI: https://doi.org/10.2210/pdb8TOX/pdb
EM Map EMD-41461: EMDB EMDataResource

Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN,IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2023-08-04 Released: 2024-08-14
Deposition Author(s): Wang, 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: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

Wang, S., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 389.08 kDa
Atom Count: 22,008
Modelled Residue Count: 2,490
Deposited Residue Count: 3,234
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A [auth B], C [auth A], E [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 12 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: 3	Glycosylation Focus chain A [auth B] Focus chain C [auth A] Focus chain E [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	B [auth G], D [auth C], F [auth I]	475	Human immunodeficiency virus 1	Mutation(s): 12 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: 18	Glycosylation Focus chain B [auth G] Focus chain D [auth C] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody ACS202 Fab heavy chain	G [auth H], I [auth D], K [auth J]	236	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody ACS202 Fab light chain	H [auth L], J [auth E], L [auth K]	214	Homo sapiens	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	AB [auth 0], BA [auth b], BB [auth 1], DA [auth d], EA [auth e], AB [auth 0], BA [auth b], BB [auth 1], DA [auth d], EA [auth e], EB [auth 4], FB [auth 5], GA [auth g], GB [auth 6], HB [auth 7], IA [auth i], JA [auth j], JB [auth 9], KA [auth k], M, N, NA [auth n], OA [auth o], P, PA [auth p], QA [auth q], R, S, SA [auth s], T, UA [auth u], VA [auth v], W, X, XA [auth x], Y, Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain T Focus chain UA [auth u] Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain T Focus chain UA [auth u] Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], DB [auth 3], FA [auth f], KB [auth AA], MA [auth m], CA [auth c], DB [auth 3], FA [auth f], KB [auth AA], MA [auth m], O, TA [auth t], V, WA [auth w]	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FA [auth f] Focus chain KB [auth AA] Focus chain MA [auth m] Focus chain O Focus chain TA [auth t] Focus chain V Focus chain WA [auth w] Interactions & Density Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FA [auth f] Focus chain KB [auth AA] Focus chain MA [auth m] Focus chain O Focus chain TA [auth t] Focus chain V Focus chain WA [auth w]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], HA [auth h], IB [auth 8], Q, RA [auth r], AA [auth a], HA [auth h], IB [auth 8], Q, RA [auth r], YA [auth y]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain HA [auth h] Focus chain IB [auth 8] Focus chain Q Focus chain RA [auth r] Focus chain YA [auth y] Interactions & Density Focus chain AA [auth a] Focus chain HA [auth h] Focus chain IB [auth 8] Focus chain Q Focus chain RA [auth r] Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CB [auth 2], LA [auth l], U	6		N-Glycosylation	Interactions Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain U Interactions & Density Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain U
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain LB [auth B] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain OB [auth G] SDF format, chain PB [auth A] SDF format, chain QB [auth C] SDF format, chain RB [auth C] SDF format, chain SB [auth C] SDF format, chain TB [auth F] SDF format, chain UB [auth I] SDF format, chain VB [auth I] SDF format, chain WB [auth I] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth C] MOL2 format, chain TB [auth F] MOL2 format, chain UB [auth I] MOL2 format, chain VB [auth I] MOL2 format, chain WB [auth I]	LB [auth B] MB [auth G] NB [auth G] OB [auth G] PB [auth A] LB [auth B], MB [auth G], NB [auth G], OB [auth G], PB [auth A], QB [auth C], RB [auth C], SB [auth C], TB [auth F], UB [auth I], VB [auth I], WB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain LB [auth B] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth F] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I] Interactions & Density Focus chain LB [auth B] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth F] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Wang, S.

Kwong, P.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

8TOX

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)