4o5i

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) 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

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 18	Fab F045-092 heavy chain × 3 （S6C4S0） Fab F045-092 light chain × 3 （P0CG05） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;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 ; × 4 ;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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 12 其他Polymer 17	Fab F045-092 heavy chain × 3 （S6C4S0） Fab F045-092 light chain × 3 （P0CG05） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R9U684_9INFA
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 G； PDBConstruct 5–323； UniProt 27–345 Author chain I； PDBConstruct 5–323； UniProt 27–345 Author chain K； 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 Author chain H； PDBConstruct 1–176； UniProt 346–521 Author chain J； PDBConstruct 1–176； UniProt 346–521 Author chain L； PDBConstruct 1–176； UniProt 346–521

Fab F045-092 heavy chain

Homo sapiens

UniProt S6C4S0

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 18	Hemagglutinin HA1 chain × 3 （R9U684） Hemagglutinin HA2 chain × 3 （R9U684） Fab F045-092 light chain × 3 （P0CG05） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;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 ; × 4 ;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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 12 其他Polymer 17	Hemagglutinin HA1 chain × 3 （R9U684） Hemagglutinin HA2 chain × 3 （R9U684） Fab F045-092 light chain × 3 （P0CG05） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6C4S0_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 150–234； UniProt 161–245 Author chain O； PDBConstruct 150–234； UniProt 161–245 Author chain Q； PDBConstruct 150–234； UniProt 161–245 Author chain S； PDBConstruct 150–234； UniProt 161–245 Author chain U； PDBConstruct 150–234； UniProt 161–245 Author chain W； PDBConstruct 150–234； UniProt 161–245

Fab F045-092 light chain

Homo sapiens

UniProt P0CG05

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 18	Hemagglutinin HA1 chain × 3 （R9U684） Hemagglutinin HA2 chain × 3 （R9U684） Fab F045-092 heavy chain × 3 （S6C4S0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ;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 ; × 4 ;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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 12 其他Polymer 17	Hemagglutinin HA1 chain × 3 （R9U684） Hemagglutinin HA2 chain × 3 （R9U684） Fab F045-092 heavy chain × 3 （S6C4S0） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LAC2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 117–216； UniProt 7–106 Author chain P； PDBConstruct 117–216； UniProt 7–106 Author chain R； PDBConstruct 117–216； UniProt 7–106 Author chain T； PDBConstruct 117–216； UniProt 7–106 Author chain V； PDBConstruct 117–216； UniProt 7–106 Author chain X； PDBConstruct 117–216； UniProt 7–106

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	4o5i
Deposition date deposition_date	2013-12-19
Structure title title	Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin
Keywords keywords	immunoglobulin, virus attachment and entry, immune recognition, VIRAL PROTEIN-IMMUNE SYSTEM complex; 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.

4o5i__assembly_1__model_1

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

Download this curve (.dat)

4o5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4o5i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	61.56 Å
Rg (electron density)	61.80 Å
Total Rg	61.63 Å
Atom count	22235
Residues	2787
Excluded volume	392380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4o5i__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4o5i__assembly_2__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 (9)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 chain
Molecular weight formula_weight	35934.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	44305

ADPGATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTR

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	1331560
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 chain
Molecular weight formula_weight	20153.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGV

Source Source

Source organism organism	Influenza A virus
NCBI taxonomy ID ncbi_taxonomy_id	1331560
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Fab F045-092 heavy chain
Molecular weight formula_weight	25719.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,O,Q,S,U,W

EVQLVESGAEVKKPGSSVKVSCRASGTFYKYAINWVRQAPGQGLEWMGGIIPFFGTTNYAQKFQGRLTITADGSTNTAYMQLDSLRSEDTAVYYCAGPSITESHYCLDCAAKDYYYGLDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

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	Fab F045-092 light chain
Molecular weight formula_weight	22626.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,P,R,T,V,X

QSVLTQPPSASGTPGQSVTISCSGSRSNIGGNTVNWYQHLPGMAPKLLIYSSNQRSSGVPDRFSGSKSGTSASLAISGLQSEDDADYYCASWDDSLNGVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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	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	13

Entity 6 Entity 6 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	15

Entity 7 Entity 7 branched

Description description	;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	910.8 kDa
Source method src_method	man
Copy count entity_count	4

Entity 8 Entity 8 branched

Description description	;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 ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 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	12

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Unit-cell length a length_a	318.123 Å
Unit-cell length b length_b	187.167 Å
Unit-cell length c length_c	353.636 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	6.501 Å
Low-resolution limit resolution_low	49.000 Å
R factor r_factor	0.2032
R_work r_work	0.2008
R_free r_free	0.2476

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) 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

Fab F045-092 heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Fab F045-092 light 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

4o5i__assembly_1__model_1

4o5i__assembly_1__model_1 | I(q)

4o5i__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 (9)

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 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

7. Citations (1)

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) 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

Fab F045-092 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

Fab F045-092 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4o5i__assembly_1__model_1

4o5i__assembly_1__model_1 | I(q)

4o5i__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 (9)

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 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

7. Citations (1)