4nm8

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

Method: X-RAY DIFFRACTION

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

Hemagglutinin HA1 Chain

Influenza A virus (strain A/Hong Kong/1/1968 H3N2)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 6	Antibody CR8043, Light Chain × 3 （P0DOX7） Antibody CR8043, Heavy Chain × 3 （Q6N089） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEMA_I68A4
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 5–323； UniProt 27–345 Author chain C； PDBConstruct 5–323； UniProt 27–345 Author chain E； PDBConstruct 5–323； UniProt 27–345 Author chain B； PDBConstruct 1–176； UniProt 346–521 Author chain D； PDBConstruct 1–176； UniProt 346–521 Author chain F； PDBConstruct 1–176； UniProt 346–521

Antibody CR8043, Light Chain

Homo sapiens

UniProt P0DOX7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 6	Hemagglutinin HA1 Chain × 3 （Q91MA7） Hemagglutinin HA2 Chain × 3 （Q91MA7） Antibody CR8043, Heavy Chain × 3 （Q6N089） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGK_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain L； PDBConstruct 121–220； UniProt 115–214 Author chain M； PDBConstruct 121–220； UniProt 115–214 Author chain N； PDBConstruct 121–220； UniProt 115–214

Antibody CR8043, Heavy Chain

Homo sapiens

UniProt Q6N089

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 6	Hemagglutinin HA1 Chain × 3 （Q91MA7） Hemagglutinin HA2 Chain × 3 （Q91MA7） Antibody CR8043, Light Chain × 3 （P0DOX7） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6N089_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 130–224； UniProt 151–245 Author chain I； PDBConstruct 130–224； UniProt 151–245 Author chain J； PDBConstruct 130–224； UniProt 151–245

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	4nm8
Deposition date deposition_date	2013-11-14
Structure title title	Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin
Keywords keywords	;Viral fusion protein, immunoglobulin, virus attachment and entry, immune recognition, viral protein-immune system complex, Immunoglobulin' ;; viral protein/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.

4nm8__assembly_1__model_1

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

Download this curve (.dat)

4nm8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nm8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.07 Å
Rg (electron density)	55.10 Å
Total Rg	55.12 Å
Atom count	21672
Residues	2757
Excluded volume	382190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nm8__assembly_1__model_1`	dodecameric （12）	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 (6)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 Chain
Molecular weight formula_weight	35506.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	21672

ADPGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTR

Source Source

Source organism organism	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
NCBI taxonomy ID ncbi_taxonomy_id	506350
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 Chain
Molecular weight formula_weight	20197.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGV

Source Source

Source organism organism	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
NCBI taxonomy ID ncbi_taxonomy_id	506350
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Antibody CR8043, Light Chain
Molecular weight formula_weight	24228.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

DIQMTQSPDSLAVSLGERATINCKSSQSVFSSSTNKNYLAWYQQKPGQPPKVLIYWSSTRESGVPDRFSASGSGTDFTLTISSLQAADVAVYYCHQYYTAPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Antibody CR8043, Heavy Chain
Molecular weight formula_weight	24753.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J

QVQLVQSGAEVKKPGASVKLSCKASGYTFTAYSMHWVRQAPGQSLEWLGWINTAIGNTQYSQKFQDRVTITRDTSARTSYMELSSLRSGDTAVYFCARGASWDARGWSGYWGKGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 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	6

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	4nm8A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	4nm8B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nm8C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	4nm8D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nm8E01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily	20 — Haemagglutinin, alpha/beta domain, HA1 chain

Domain ID domain_id	4nm8F00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4nm8H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8J01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8J02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8M01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8M02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8N01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4nm8N02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	241.491 Å
Unit-cell length b length_b	142.355 Å
Unit-cell length c length_c	170.725 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	133.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	4.004 Å
Low-resolution limit resolution_low	43.821 Å
R factor r_factor	0.2423
R_work r_work	0.2397
R_free r_free	0.2924

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

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

Hemagglutinin HA1 Chain

State in the Current Structure

Other States of the Same Protein in the Database

Antibody CR8043, Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Antibody CR8043, Heavy Chain

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

4nm8__assembly_1__model_1

4nm8__assembly_1__model_1 | I(q)

4nm8__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 (6)

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 branched

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

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

Hemagglutinin HA1 Chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Antibody CR8043, Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Antibody CR8043, Heavy Chain

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

4nm8__assembly_1__model_1

4nm8__assembly_1__model_1 | I(q)

4nm8__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 (6)

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 branched

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)