3M6S | pdb_00003m6s

Crystal structure of H1N1pdm Hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb3M6S/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Darwin/2001/2009(H1N1))
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2010-03-16 Released: 2010-03-31
Deposition Author(s): Yang, H., Carney, P.J., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.256 (Depositor), 0.251 (DCC)
R-Value Work:
0.230 (Depositor), 0.227 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin

Yang, H., Carney, P., Stevens, J.

(2010) PLoS Curr : RRN1152-RRN1152

PubMed: 20352039 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/currents.RRN1152
Primary Citation Related Structures:
3M6S

PubMed Abstract:
The 3D-structure of the major surface viral antigen from the recent H1N1 pandemic influenza virus (A/Darwin/2001/2009) was determined to 2.8 Å resolution. The structure was used to analyze changes in the HA that have emerged during the first 11 months of the pandemic and have raised public health concerns. Receptor binding properties of this protein reveals a strict preference for human-type receptors.

Organizational Affiliation

Centers for Disease Control and Prevention.

Macromolecule Content

Total Structure Weight: 347.69 kDa
Atom Count: 23,587
Modeled Residue Count: 2,958
Deposited Residue Count: 3,072
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E, G, I A, C, E, G, I, K	331	Influenza A virus (A/Darwin/2001/2009(H1N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for C5MV42 (Influenza A virus) Explore C5MV42 Go to UniProtKB: C5MV42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5MV42
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E Focus chain G Focus chain I Focus chain K
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H, J B, D, F, H, J, L	181	Influenza A virus (A/Darwin/2001/2009(H1N1))	Mutation(s): 3 Gene Names: HA
UniProt
Find proteins for C5MV42 (Influenza A virus) Explore C5MV42 Go to UniProtKB: C5MV42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5MV42
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	3		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 1 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 T [auth G] SDF format, chain U [auth G] SDF format, chain S [auth E] MOL2 format, chain R [auth A] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain S [auth E] mmCIF format, chain R [auth A] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain S [auth E]	R [auth A], S [auth E], T [auth G], U [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth A] Focus chain S [auth E] Focus chain T [auth G] Focus chain U [auth G] Interactions & Density Focus chain R [auth A] Focus chain S [auth E] Focus chain T [auth G] Focus chain U [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.256 (Depositor), 0.251 (DCC)
R-Value Work: 0.230 (Depositor), 0.227 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.984	α = 86.25
b = 109.709	β = 74.68
c = 129.896	γ = 75.1

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Yang, H.

Carney, P.J.

Stevens, J.

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2014-03-19
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
Version 2.1: 2021-10-06
Changes: Advisory, Database references, Structure summary
Version 2.2: 2023-09-06
Changes: Data collection, Refinement description
Version 2.3: 2024-11-27
Changes: Structure summary