4HLZ

Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb4HLZ/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus (A/Japan/305/1957(H2N2)), Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2012-10-17 Released: 2013-04-17
Deposition Author(s): Dreyfus, C., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.284
R-Value Work: 0.228
R-Value Observed: 0.231

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structure of a classical broadly neutralizing stem antibody in complex with a pandemic h2 influenza virus hemagglutinin.

Dreyfus, C., Ekiert, D.C., Wilson, I.A.

(2013) J Virol 87: 7149-7154

PubMed: 23552413 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.02975-12
Primary Citation of Related Structures:
4HLZ

PubMed Abstract:
We report the structural characterization of the first antibody identified to cross-neutralize multiple subtypes of influenza A viruses. The crystal structure of mouse antibody C179 bound to the pandemic 1957 H2N2 hemagglutinin (HA) reveals that it targets an epitope on the HA stem similar to those targeted by the recently identified human broadly neutralizing antibodies. C179 also inhibits the low-pH conformational change of the HA but uses a different angle of approach and both heavy and light chains.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.

Macromolecule Content

Total Structure Weight: 319.54 kDa
Atom Count: 21,839
Modelled Residue Count: 2,754
Deposited Residue Count: 2,832
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	327	Influenza A virus (A/Japan/305/1957(H2N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2)) Explore C7S226 Go to UniProtKB: C7S226
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7S226
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F	174	Influenza A virus (A/Japan/305/1957(H2N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C7S226 (Influenza A virus (strain A/Japan/305/1957 H2N2)) Explore C7S226 Go to UniProtKB: C7S226
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7S226
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain F
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C179 heavy chain	G, I, K	229	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C179 light chain	H, J, L	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, P	3		N-Glycosylation	Interactions Focus chain M Focus chain P Interactions & Density Focus chain M Focus chain P
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	N	4		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, Q	2		N-Glycosylation	Interactions Focus chain O Focus chain Q Interactions & Density Focus chain O Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth B] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	R [auth A], S [auth A], U [auth B], W [auth E], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain W [auth E] Focus chain Z [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain BA [auth J] SDF format, chain DA [auth L] SDF format, chain T [auth B] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth F] MOL2 format, chain AA [auth H] MOL2 format, chain BA [auth J] MOL2 format, chain DA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth H] mmCIF format, chain BA [auth J] mmCIF format, chain DA [auth L] mmCIF format, chain T [auth B] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth F]	AA [auth H] BA [auth J] DA [auth L] T [auth B] V [auth D] AA [auth H], BA [auth J], DA [auth L], T [auth B], V [auth D], X [auth E], Y [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth H] Focus chain BA [auth J] Focus chain DA [auth L] Focus chain T [auth B] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth J] Focus chain DA [auth L] Focus chain T [auth B] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth J] MOL2 format, chain CA [auth J] mmCIF format, chain CA [auth J]	CA [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Interactions & Density Focus chain CA [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.284
R-Value Work: 0.228
R-Value Observed: 0.231
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.58	α = 90
b = 150.78	β = 90
c = 217.78	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Dreyfus, C.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2013-07-24
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary