9mmj

Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein

Method: X-RAY DIFFRACTION

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

Surface protein gp120 JR-FL V3 peptide

OrganismNot specified

UniProt P20871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	19b Fab Light Chain × 1 19b Fab Heavy Chain × 1 ACETATE ION × 1 GLYCEROL × 2 SULFATE ION × 2 SODIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENV_HV1JR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–43； UniProt 291–333

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	9mmj
Deposition date deposition_date	2024-12-20
Last revision last_revision	2026-01-21
Structure title title	Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein
Keywords keywords	19b, Fab, Fragment antigen-binding, HIV-1 Envelope, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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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.

9mmj__assembly_1__model_1

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

Download this curve (.dat)

9mmj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9mmj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.19 Å
Rg (electron density)	24.11 Å
Total Rg	24.92 Å
Atom count	3331
Residues	439
Excluded volume	58799 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9mmj__assembly_1__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	19b Fab Light Chain
Molecular weight formula_weight	23201.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3853

DIVLTQSPPSLSASVGDRVTITCQASQDISDHLSWFQQKPGKAPKLLVYGVSSLEAGVPSRFSVSGSGTHFTFTVNGLQPEDLATYFCQQYDDLPWTFGPGTVVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	19b Fab Heavy Chain
Molecular weight formula_weight	22791.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLVQSGGALIQPGGSLRLSCAASGFTFVDYAMSWVRQAPGKGLQWVSTIIGSGADTYYTDSVKGRFTISRDNSNNTVHLQMNSLRADDTALYYCVRGVFDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Surface protein gp120 JR-FL V3 peptide
Molecular weight formula_weight	4919.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

EINCTRPNNNTRKSIHIGPGRWFYTTGEIIGDIRQAHCNISRA

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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Unit-cell length a length_a	45.902 Å
Unit-cell length b length_b	87.507 Å
Unit-cell length c length_c	131.973 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	34.610 Å
R factor r_factor	0.1607
R_work r_work	0.1588
R_free r_free	0.1989

Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein

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

Surface protein gp120 JR-FL V3 peptide

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

9mmj__assembly_1__model_1

9mmj__assembly_1__model_1 | I(q)

9mmj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal Structure of 19b Fab bound to the third variable (V3) loop peptide from the HIV-1 JR-FL envelope (Env) glycoprotein

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

Surface protein gp120 JR-FL V3 peptide

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

9mmj__assembly_1__model_1

9mmj__assembly_1__model_1 | I(q)

9mmj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)