7MXD | pdb_00007mxd

Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 Env

PDB DOI: https://doi.org/10.2210/pdb7MXD/pdb
EM Map EMD-24071: EMDB EMDataResource

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

Deposited: 2021-05-19 Released: 2022-03-30
Deposition Author(s): Zhou, T., Gao, F.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Development of Neutralization Breadth against Diverse HIV-1 by Increasing Ab-Ag Interface on V2.

Gao, N., Gai, Y., Meng, L., Wang, C., Wang, W., Li, X., Gu, T., Louder, M.K., Doria-Rose, N.A., Wiehe, K., Nazzari, A.F., Olia, A.S., Gorman, J., Rawi, R., Wu, W., Smith, C., Khant, H., de Val, N., Yu, B., Luo, J., Niu, H., Tsybovsky, Y., Liao, H., Kepler, T.B., Kwong, P.D., Mascola, J.R., Qin, C., Zhou, T., Yu, X., Gao, F.

(2022) Adv Sci (Weinh) 9: e2200063-e2200063

PubMed: 35319830 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/advs.202200063
Primary Citation Related Structures:
7MXD, 7N28

PubMed Abstract:
Understanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 can be highly informative for HIV-1 vaccine development. A lineage of J038 bnAbs is now obtained from a long-term SHIV-infected macaque. J038 neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique "up" conformation for one of the V2 loops in the trimeric envelope glycoprotein and is heavily dependent on glycan, which provides nearly half of the binding surface. Their unmutated common ancestor neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for elicitation and maturation of V2-targeting bnAbs.

Organizational Affiliation

National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China.

Macromolecule Content

Total Structure Weight: 434.22 kDa
Atom Count: 29,496
Modeled Residue Count: 3,519
Deposited Residue Count: 3,631
Unique protein chains: 6

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, D [auth F], E [auth G]	478	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for I6NF57 (Human immunodeficiency virus type 1) Explore I6NF57 Go to UniProtKB: I6NF57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6NF57
Glycosylation
Glycosylation Sites: 20	Glycosylation Focus chain A Focus chain D [auth F] Focus chain E [auth G]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3BNC117 antibody heavy chain	B [auth C], F [auth J], H [auth S]	226	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3BNC117 antibody light chain	C [auth D], G [auth K], I [auth U]	206	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
J038 antibody heavy chain	J [auth X]	228	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
J038 antibody light chain	K [auth Y]	214	Macaca mulatta	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	L [auth B], M [auth I], N [auth H]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for I6NF57 (Human immunodeficiency virus type 1) Explore I6NF57 Go to UniProtKB: I6NF57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6NF57
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain L [auth B] Focus chain M [auth I] Focus chain N [auth H]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 7
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 a], BA [auth b], CA [auth c], FA [auth f], GA [auth g], AA [auth a], BA [auth b], CA [auth c], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], NA [auth n], O [auth E], P [auth L], Q [auth M], QA [auth q], RA [auth r], SA [auth s], T [auth P], TA [auth t], UA [auth u], V [auth R], VA [auth v], W [auth T], WA [auth w], X [auth V], Y [auth W], Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain O [auth E] Focus chain P [auth L] Focus chain Q [auth M] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T [auth P] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain V [auth R] Focus chain VA [auth v] Focus chain W [auth T] Focus chain WA [auth w] Focus chain X [auth V] Focus chain Y [auth W] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain O [auth E] Focus chain P [auth L] Focus chain Q [auth M] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T [auth P] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain V [auth R] Focus chain VA [auth v] Focus chain W [auth T] Focus chain WA [auth w] Focus chain X [auth V] Focus chain Y [auth W] Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	R [auth N]	8		N-Glycosylation	Interactions Focus chain R [auth N] Interactions & Density Focus chain R [auth N]
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

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	EA [auth e], MA [auth m], PA [auth p], S [auth O]	7		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain S [auth O] Interactions & Density Focus chain EA [auth e] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain S [auth O]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 10
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	U [auth Q]	3		N-Glycosylation	Interactions Focus chain U [auth Q] Interactions & Density Focus chain U [auth Q]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	DA [auth d], OA [auth o]	6		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain OA [auth o] Interactions & Density Focus chain DA [auth d] Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 2 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 A] SDF format, chain AC [auth K] SDF format, chain BB [auth A] SDF format, chain BC [auth U] SDF format, chain CB [auth A] SDF format, chain CC [auth B] SDF format, chain DB [auth A] SDF format, chain DC [auth B] SDF format, chain EB [auth A] SDF format, chain EC [auth B] SDF format, chain FC [auth B] SDF format, chain GC [auth I] SDF format, chain HC [auth I] SDF format, chain IC [auth I] SDF format, chain JB [auth F] SDF format, chain KC [auth H] SDF format, chain LB [auth F] SDF format, chain LC [auth H] SDF format, chain MB [auth F] SDF format, chain NB [auth F] SDF format, chain OB [auth F] SDF format, chain PB [auth F] SDF format, chain QB [auth F] SDF format, chain RB [auth G] SDF format, chain SB [auth G] SDF format, chain TB [auth G] SDF format, chain UB [auth G] SDF format, chain VB [auth G] SDF format, chain WB [auth G] SDF format, chain XA [auth A] SDF format, chain XB [auth G] SDF format, chain YA [auth A] SDF format, chain YB [auth G] SDF format, chain ZA [auth A] SDF format, chain ZB [auth G] SDF format, chain KB [auth F] SDF format, chain JC [auth H] SDF format, chain GB [auth D] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth K] MOL2 format, chain BB [auth A] MOL2 format, chain BC [auth U] MOL2 format, chain CB [auth A] MOL2 format, chain CC [auth B] MOL2 format, chain DB [auth A] MOL2 format, chain DC [auth B] MOL2 format, chain EB [auth A] MOL2 format, chain EC [auth B] MOL2 format, chain FC [auth B] MOL2 format, chain GC [auth I] MOL2 format, chain HC [auth I] MOL2 format, chain IC [auth I] MOL2 format, chain JB [auth F] MOL2 format, chain KC [auth H] MOL2 format, chain LB [auth F] MOL2 format, chain LC [auth H] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain OB [auth F] MOL2 format, chain PB [auth F] MOL2 format, chain QB [auth F] MOL2 format, chain RB [auth G] MOL2 format, chain SB [auth G] MOL2 format, chain TB [auth G] MOL2 format, chain UB [auth G] MOL2 format, chain VB [auth G] MOL2 format, chain WB [auth G] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth G] MOL2 format, chain YA [auth A] MOL2 format, chain YB [auth G] MOL2 format, chain ZA [auth A] MOL2 format, chain ZB [auth G] MOL2 format, chain KB [auth F] MOL2 format, chain JC [auth H] MOL2 format, chain GB [auth D] mmCIF format, chain AB [auth A] mmCIF format, chain AC [auth K] mmCIF format, chain BB [auth A] mmCIF format, chain BC [auth U] mmCIF format, chain CB [auth A] mmCIF format, chain CC [auth B] mmCIF format, chain DB [auth A] mmCIF format, chain DC [auth B] mmCIF format, chain EB [auth A] mmCIF format, chain EC [auth B] mmCIF format, chain FC [auth B] mmCIF format, chain GC [auth I] mmCIF format, chain HC [auth I] mmCIF format, chain IC [auth I] mmCIF format, chain JB [auth F] mmCIF format, chain KC [auth H] mmCIF format, chain LB [auth F] mmCIF format, chain LC [auth H] mmCIF format, chain MB [auth F] mmCIF format, chain NB [auth F] mmCIF format, chain OB [auth F] mmCIF format, chain PB [auth F] mmCIF format, chain QB [auth F] mmCIF format, chain RB [auth G] mmCIF format, chain SB [auth G] mmCIF format, chain TB [auth G] mmCIF format, chain UB [auth G] mmCIF format, chain VB [auth G] mmCIF format, chain WB [auth G] mmCIF format, chain XA [auth A] mmCIF format, chain XB [auth G] mmCIF format, chain YA [auth A] mmCIF format, chain YB [auth G] mmCIF format, chain ZA [auth A] mmCIF format, chain ZB [auth G] mmCIF format, chain KB [auth F] mmCIF format, chain JC [auth H] mmCIF format, chain GB [auth D]	AB [auth A] AC [auth K] BB [auth A] BC [auth U] CB [auth A] AB [auth A], AC [auth K], BB [auth A], BC [auth U], CB [auth A], CC [auth B], DB [auth A], DC [auth B], EB [auth A], EC [auth B], FC [auth B], GB [auth D], GC [auth I], HC [auth I], IC [auth I], JB [auth F], JC [auth H], KB [auth F], KC [auth H], LB [auth F], LC [auth H], MB [auth F], NB [auth F], OB [auth F], PB [auth F], QB [auth F], RB [auth G], SB [auth G], TB [auth G], UB [auth G], VB [auth G], WB [auth G], XA [auth A], XB [auth G], YA [auth A], YB [auth G], ZA [auth A], ZB [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain AC [auth K] Focus chain BB [auth A] Focus chain BC [auth U] Focus chain CB [auth A] Focus chain CC [auth B] Focus chain DB [auth A] Focus chain DC [auth B] Focus chain EB [auth A] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GB [auth D] Focus chain GC [auth I] Focus chain HC [auth I] Focus chain IC [auth I] Focus chain JB [auth F] Focus chain JC [auth H] Focus chain KB [auth F] Focus chain KC [auth H] Focus chain LB [auth F] Focus chain LC [auth H] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain VB [auth G] Focus chain WB [auth G] Focus chain XA [auth A] Focus chain XB [auth G] Focus chain YA [auth A] Focus chain YB [auth G] Focus chain ZA [auth A] Focus chain ZB [auth G] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth K] Focus chain BB [auth A] Focus chain BC [auth U] Focus chain CB [auth A] Focus chain CC [auth B] Focus chain DB [auth A] Focus chain DC [auth B] Focus chain EB [auth A] Focus chain EC [auth B] Focus chain FC [auth B] Focus chain GB [auth D] Focus chain GC [auth I] Focus chain HC [auth I] Focus chain IC [auth I] Focus chain JB [auth F] Focus chain JC [auth H] Focus chain KB [auth F] Focus chain KC [auth H] Focus chain LB [auth F] Focus chain LC [auth H] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain OB [auth F] Focus chain PB [auth F] Focus chain QB [auth F] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain VB [auth G] Focus chain WB [auth G] Focus chain XA [auth A] Focus chain XB [auth G] Focus chain YA [auth A] Focus chain YB [auth G] Focus chain ZA [auth A] Focus chain ZB [auth G]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain FB [auth A] SDF format, chain HB [auth F] SDF format, chain IB [auth F] MOL2 format, chain FB [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth F] mmCIF format, chain FB [auth A] mmCIF format, chain HB [auth F] mmCIF format, chain IB [auth F]	FB [auth A], HB [auth F], IB [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FB [auth A] Focus chain HB [auth F] Focus chain IB [auth F] Interactions & Density Focus chain FB [auth A] Focus chain HB [auth F] Focus chain IB [auth F]