6V6W | pdb_00006v6w

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22

PDB DOI: https://doi.org/10.2210/pdb6V6W/pdb

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

Deposited: 2019-12-06 Released: 2020-09-23
Deposition Author(s): Kumar, S., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 6.50 Å
R-Value Free:
0.355 (Depositor), 0.355 (DCC)
R-Value Work:
0.309 (Depositor), 0.310 (DCC)
R-Value Observed:
0.311 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

Kumar, S., Ju, B., Shapero, B., Lin, X., Ren, L., Zhang, L., Li, D., Zhou, Z., Feng, Y., Sou, C., Mann, C.J., Hao, Y., Sarkar, A., Hou, J., Nunnally, C., Hong, K., Wang, S., Ge, X., Su, B., Landais, E., Sok, D., Zwick, M.B., He, L., Zhu, J., Wilson, I.A., Shao, Y.

(2020) Sci Adv 6: eabb1328

DOI: https://doi.org/10.1126/sciadv.abb1328

Macromolecule Content

Total Structure Weight: 344.68 kDa
Atom Count: 23,434
Modeled Residue Count: 2,958
Deposited Residue Count: 3,068
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab Heavy chain	A [auth D], G [auth A]	243	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
35O22 Fab Light chain	B [auth E], H [auth B]	216	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C [auth G], I [auth C]	485	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain C [auth G] Focus chain I [auth C]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
B11 DSS Fab heavy chain	D [auth I], J [auth F]	235	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
B11 Fab light chain	E [auth J], K [auth H]	215	Human immunodeficiency virus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	F [auth T], L [auth K]	140	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus type 1) Explore Q2N0S9 Go to UniProtKB: Q2N0S9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S9
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain F [auth T] Focus chain L [auth K]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	M [auth L], P [auth O]	4		N-Glycosylation	Interactions Focus chain M [auth L] Focus chain P [auth O] Interactions & Density Focus chain M [auth L] Focus chain P [auth O]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth M], Q [auth P]	2		N-Glycosylation	Interactions Focus chain N [auth M] Focus chain Q [auth P] Interactions & Density Focus chain N [auth M] Focus chain Q [auth P]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	O [auth N], R [auth Q]	5		N-Glycosylation	Interactions Focus chain O [auth N] Focus chain R [auth Q] Interactions & Density Focus chain O [auth N] Focus chain R [auth Q]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 AA [auth G] SDF format, chain BA [auth T] SDF format, chain CA [auth T] SDF format, chain DA [auth T] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth K] SDF format, chain OA [auth K] SDF format, chain PA [auth K] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth T] MOL2 format, chain CA [auth T] MOL2 format, chain DA [auth T] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth K] MOL2 format, chain PA [auth K] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth T] mmCIF format, chain CA [auth T] mmCIF format, chain DA [auth T] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth K] mmCIF format, chain PA [auth K] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	AA [auth G] BA [auth T] CA [auth T] DA [auth T] EA [auth C] AA [auth G], BA [auth T], CA [auth T], DA [auth T], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth K], OA [auth K], PA [auth K], S [auth G], T [auth G], U [auth G], V [auth G], W [auth G], X [auth G], Y [auth G], Z [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth T] Focus chain CA [auth T] Focus chain DA [auth T] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth K] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth T] Focus chain CA [auth T] Focus chain DA [auth T] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth K] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 6.50 Å
R-Value Free: 0.355 (Depositor), 0.355 (DCC)
R-Value Work: 0.309 (Depositor), 0.310 (DCC)
R-Value Observed: 0.311 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.534	α = 90
b = 148.534	β = 90
c = 843.554	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
HKL-2000	data processing
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Kumar, S.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2020-09-23
Type: Initial release
Version 1.1: 2021-01-27
Changes: Derived calculations
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary