9pit

HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp160

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 18 其他Polymer 33	1-23 light chain Fv × 3 1-23 heavy chain Fv × 3 RM19R light chain Fv × 3 RM19R heavy chain Fv × 3 Envelope glycoprotein gp41 - BG505 MD39 × 3 （Q2N0S8） ;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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 24 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2N0S5_HV1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 32–512； UniProt 30–510 Author chain E； PDBConstruct 32–512； UniProt 30–510 Author chain F； PDBConstruct 32–512； UniProt 30–510

Envelope glycoprotein gp41 - BG505 MD39

Human immunodeficiency virus 1

UniProt Q2N0S8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 18 其他Polymer 33	1-23 light chain Fv × 3 1-23 heavy chain Fv × 3 Envelope glycoprotein gp160 × 3 （Q2N0S5） RM19R light chain Fv × 3 RM19R heavy chain Fv × 3 ;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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 24 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2N0S8_9HIV1
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 511–663 Author chain C； PDBConstruct 1–153； UniProt 511–663 Author chain D； PDBConstruct 1–153； UniProt 511–663

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pit
Deposition date deposition_date	2025-07-11
Structure title title	HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R
Keywords keywords	HIV-1, SOSIP, human, broadly neutralizing antibody, Fab, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9pit__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pit__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pit__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	50.16 Å
Rg (electron density)	49.71 Å
Total Rg	49.97 Å
Atom count	25533
Residues	3075
Excluded volume	451940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pit__assembly_1__model_1`	18-meric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	1-23 light chain Fv
Molecular weight formula_weight	11722.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,Q,R
Atom count atom_count	25533

EPVLTQSPGTLSLSPGEGATLSCRARQGFSADHVAWFQKKPGRPPRLLIFEASRRASGTPERFSGGGSGPEYTLTITRVEPEDFAVYYCQSYGSITPLVFGGGTRVDVK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	1-23 heavy chain Fv
Molecular weight formula_weight	14166.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,M,N

QLVQSGGGVRRPGASVKISCETPEYTFTKYWLHWLRQAPGRGLEWMGVVSPHGGRPMFAFEFRDRLTLTRDIHTTTHYMELRGLTSDDTAVYFCARDSFGETFRGHDQPYQMDVWGGGTTVVVSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein gp160
Molecular weight formula_weight	57141.0 kDa
Mutation mutation	T106E, M271I, F288L, R304V, A319Y, T332N, N363Q, A501C, E509R, K510R, A512R, V513R
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,F

MGILPSPGMPALLSLVSLLSVLLMGCVAETGAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	RM19R light chain Fv
Molecular weight formula_weight	11808.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I,K

AIRMTQSPAILSLSPGERATLSCRASQSVDSRLAWYQQKPGQSPRLLIYDVSSRATGIPDRFSGSGSGTEFTLTISSLEPEDVAVYFCHQENDWPWTFGQGTKVEIK

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	RM19R heavy chain Fv
Molecular weight formula_weight	13268.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,O,P

EVQLVESGPGLVRPSETLSLTCAVSGDSISTNNGWSWIRQTPGKGLEWIGYINGRSGSTRYNPSLQSRVTISTDTSGNQFSLKVNSVTAADTAKYYCAFFWSTYYKRFDVWGPGVRVTVSS

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Envelope glycoprotein gp41 - BG505 MD39
Molecular weight formula_weight	18250.5 kDa
Mutation mutation	F519S, I559P, A561P, L568D, V570H, R585H, T605C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D

AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGTKHHHHHH

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 branched

Description description	;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 ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 8 Entity 8 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	24

Entity 9 Entity 9 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	6

Entity 10 Entity 10 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	21

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Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	500071

HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp160

State in the Current Structure

Other States of the Same Protein in the Database

Envelope glycoprotein gp41 - BG505 MD39

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pit__assembly_1__model_1

9pit__assembly_1__model_1 | I(q)

9pit__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 non-polymer

7. Citations (1)

HIV-1 bnAb 1-23 in complex with BG505 MD39 SOSIP and RM19R

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp160

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein gp41 - BG505 MD39

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pit__assembly_1__model_1

9pit__assembly_1__model_1 | I(q)

9pit__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 non-polymer

7. Citations (1)