9ZRY | pdb_00009zry

Cryo-EM structure of SHIV-elicited CN81-2029 Fab in complex with HIV Env trimer Q23-SCT27

PDB DOI: https://doi.org/10.2210/pdb9ZRY/pdb
EM Map EMD-74655: EMDB EMDataResource

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

Deposited: 2025-12-21 Released: 2026-06-03
Deposition Author(s): Roark, R.S., Shapiro, L., 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: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 Å
Resolution: 2.90 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

Enhanced Priming Leads to Rapid Induction of Broadly Neutralizing HIV-1 Apex Antibodies

Roark, R.S., Shapiro, L., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 298.18 kDa
Atom Count: 17,248
Modeled Residue Count: 1,961
Deposited Residue Count: 2,431
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CN81-2029 heavy chain	A	243	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CN81-2029 light chain	B	220	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope gp120	C [auth b], E [auth d], G [auth f]	503	Human immunodeficiency virus	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain C [auth b] Focus chain E [auth d] Focus chain G [auth f]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope gp41 ectodomain	D [auth c], F [auth e], H [auth g]	153	Human immunodeficiency virus	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for O55774 (Human immunodeficiency virus type 1) Explore O55774 Go to UniProtKB: O55774
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O55774
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D [auth c] Focus chain F [auth e] Focus chain H [auth g]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth U], BA [auth V], CA [auth W], DA [auth X], EA [auth Y], AA [auth U], BA [auth V], CA [auth W], DA [auth X], EA [auth Y], FA [auth Z], GA [auth a], HA [auth h], I [auth C], KA [auth k], L [auth F], MA [auth m], N [auth H], NA [auth n], O [auth I], OA [auth o], PA [auth p], Q [auth K], QA [auth q], R [auth L], RA [auth r], S [auth M], SA [auth s], T [auth N], U [auth O], X [auth R], Y [auth S], Z [auth T]	2		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain BA [auth V] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth h] Focus chain I [auth C] Focus chain KA [auth k] Focus chain L [auth F] Focus chain MA [auth m] Focus chain N [auth H] Focus chain NA [auth n] Focus chain O [auth I] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth K] Focus chain QA [auth q] Focus chain R [auth L] Focus chain RA [auth r] Focus chain S [auth M] Focus chain SA [auth s] Focus chain T [auth N] Focus chain U [auth O] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T] Interactions & Density Focus chain AA [auth U] Focus chain BA [auth V] Focus chain CA [auth W] Focus chain DA [auth X] Focus chain EA [auth Y] Focus chain FA [auth Z] Focus chain GA [auth a] Focus chain HA [auth h] Focus chain I [auth C] Focus chain KA [auth k] Focus chain L [auth F] Focus chain MA [auth m] Focus chain N [auth H] Focus chain NA [auth n] Focus chain O [auth I] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain Q [auth K] Focus chain QA [auth q] Focus chain R [auth L] Focus chain RA [auth r] Focus chain S [auth M] Focus chain SA [auth s] Focus chain T [auth N] Focus chain U [auth O] Focus chain X [auth R] Focus chain Y [auth S] Focus chain Z [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	IA [auth i], J [auth D], P [auth J], V [auth P]	3		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain J [auth D] Focus chain P [auth J] Focus chain V [auth P] Interactions & Density Focus chain IA [auth i] Focus chain J [auth D] Focus chain P [auth J] Focus chain V [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
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	JA [auth j], K [auth E], W [auth Q]	5		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain K [auth E] Focus chain W [auth Q] Interactions & Density Focus chain JA [auth j] Focus chain K [auth E] Focus chain W [auth Q]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	M [auth G]	4		N-Glycosylation	Interactions Focus chain M [auth G] Interactions & Density Focus chain M [auth G]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	LA [auth l]	7		N-Glycosylation	Interactions Focus chain LA [auth l] Interactions & Density Focus chain LA [auth l]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

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 ZA [auth b] SDF format, chain YB [auth g] SDF format, chain YA [auth b] SDF format, chain XB [auth g] SDF format, chain XA [auth b] SDF format, chain WB [auth g] SDF format, chain WA [auth b] SDF format, chain VB [auth f] SDF format, chain VA [auth b] SDF format, chain UB [auth f] SDF format, chain UA [auth b] SDF format, chain TB [auth f] SDF format, chain TA [auth b] SDF format, chain SB [auth f] SDF format, chain RB [auth f] SDF format, chain QB [auth f] SDF format, chain PB [auth f] SDF format, chain OB [auth f] SDF format, chain NB [auth e] SDF format, chain MB [auth e] SDF format, chain LB [auth e] SDF format, chain KB [auth d] SDF format, chain JB [auth d] SDF format, chain IB [auth d] SDF format, chain HB [auth d] SDF format, chain GB [auth d] SDF format, chain FB [auth d] SDF format, chain EB [auth d] SDF format, chain DB [auth c] SDF format, chain CB [auth c] SDF format, chain BB [auth c] SDF format, chain AB [auth b] MOL2 format, chain ZA [auth b] MOL2 format, chain YB [auth g] MOL2 format, chain YA [auth b] MOL2 format, chain XB [auth g] MOL2 format, chain XA [auth b] MOL2 format, chain WB [auth g] MOL2 format, chain WA [auth b] MOL2 format, chain VB [auth f] MOL2 format, chain VA [auth b] MOL2 format, chain UB [auth f] MOL2 format, chain UA [auth b] MOL2 format, chain TB [auth f] MOL2 format, chain TA [auth b] MOL2 format, chain SB [auth f] MOL2 format, chain RB [auth f] MOL2 format, chain QB [auth f] MOL2 format, chain PB [auth f] MOL2 format, chain OB [auth f] MOL2 format, chain NB [auth e] MOL2 format, chain MB [auth e] MOL2 format, chain LB [auth e] MOL2 format, chain KB [auth d] MOL2 format, chain JB [auth d] MOL2 format, chain IB [auth d] MOL2 format, chain HB [auth d] MOL2 format, chain GB [auth d] MOL2 format, chain FB [auth d] MOL2 format, chain EB [auth d] MOL2 format, chain DB [auth c] MOL2 format, chain CB [auth c] MOL2 format, chain BB [auth c] MOL2 format, chain AB [auth b] mmCIF format, chain ZA [auth b] mmCIF format, chain YB [auth g] mmCIF format, chain YA [auth b] mmCIF format, chain XB [auth g] mmCIF format, chain XA [auth b] mmCIF format, chain WB [auth g] mmCIF format, chain WA [auth b] mmCIF format, chain VB [auth f] mmCIF format, chain VA [auth b] mmCIF format, chain UB [auth f] mmCIF format, chain UA [auth b] mmCIF format, chain TB [auth f] mmCIF format, chain TA [auth b] mmCIF format, chain SB [auth f] mmCIF format, chain RB [auth f] mmCIF format, chain QB [auth f] mmCIF format, chain PB [auth f] mmCIF format, chain OB [auth f] mmCIF format, chain NB [auth e] mmCIF format, chain MB [auth e] mmCIF format, chain LB [auth e] mmCIF format, chain KB [auth d] mmCIF format, chain JB [auth d] mmCIF format, chain IB [auth d] mmCIF format, chain HB [auth d] mmCIF format, chain GB [auth d] mmCIF format, chain FB [auth d] mmCIF format, chain EB [auth d] mmCIF format, chain DB [auth c] mmCIF format, chain CB [auth c] mmCIF format, chain BB [auth c] mmCIF format, chain AB [auth b]	AB [auth b] BB [auth c] CB [auth c] DB [auth c] EB [auth d] AB [auth b], BB [auth c], CB [auth c], DB [auth c], EB [auth d], FB [auth d], GB [auth d], HB [auth d], IB [auth d], JB [auth d], KB [auth d], LB [auth e], MB [auth e], NB [auth e], OB [auth f], PB [auth f], QB [auth f], RB [auth f], SB [auth f], TA [auth b], TB [auth f], UA [auth b], UB [auth f], VA [auth b], VB [auth f], WA [auth b], WB [auth g], XA [auth b], XB [auth g], YA [auth b], YB [auth g], ZA [auth b]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth b] Focus chain BB [auth c] Focus chain CB [auth c] Focus chain DB [auth c] Focus chain EB [auth d] Focus chain FB [auth d] Focus chain GB [auth d] Focus chain HB [auth d] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth e] Focus chain MB [auth e] Focus chain NB [auth e] Focus chain OB [auth f] Focus chain PB [auth f] Focus chain QB [auth f] Focus chain RB [auth f] Focus chain SB [auth f] Focus chain TA [auth b] Focus chain TB [auth f] Focus chain UA [auth b] Focus chain UB [auth f] Focus chain VA [auth b] Focus chain VB [auth f] Focus chain WA [auth b] Focus chain WB [auth g] Focus chain XA [auth b] Focus chain XB [auth g] Focus chain YA [auth b] Focus chain YB [auth g] Focus chain ZA [auth b] Interactions & Density Focus chain AB [auth b] Focus chain BB [auth c] Focus chain CB [auth c] Focus chain DB [auth c] Focus chain EB [auth d] Focus chain FB [auth d] Focus chain GB [auth d] Focus chain HB [auth d] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth d] Focus chain LB [auth e] Focus chain MB [auth e] Focus chain NB [auth e] Focus chain OB [auth f] Focus chain PB [auth f] Focus chain QB [auth f] Focus chain RB [auth f] Focus chain SB [auth f] Focus chain TA [auth b] Focus chain TB [auth f] Focus chain UA [auth b] Focus chain UB [auth f] Focus chain VA [auth b] Focus chain VB [auth f] Focus chain WA [auth b] Focus chain WB [auth g] Focus chain XA [auth b] Focus chain XB [auth g] Focus chain YA [auth b] Focus chain YB [auth g] Focus chain ZA [auth b]