PDB-2wr7: the structure of influenza H2 human singapore hemagglutinin with ...

ID or keywords:

Entry

Database: PDB / ID: 2wr7

Title

the structure of influenza H2 human singapore hemagglutinin with human receptor

Components

HEMAGGLUTININ

Keywords

VIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / LIPROPROTEIN

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function

Biological species

INFLUENZA A VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.5 Å

Authors

Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.

History

Deposition	Aug 30, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wr7.cif.gz	572 KB	Display	PDBx/mmCIF format
PDB format	pdb2wr7.ent.gz	474 KB	Display	PDB format
PDBx/mmJSON format	2wr7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2wr7_validation.pdf.gz	873 KB	Display	wwPDB validaton report
Full document	2wr7_full_validation.pdf.gz	913.2 KB	Display
Data in XML	2wr7_validation.xml.gz	65.3 KB	Display
Data in CIF	2wr7_validation.cif.gz	85.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wr7 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wr7	HTTPS FTP

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Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr4C 2wr5C 2wrbC 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	4ju0-2 1rvz-2 2wrc-d 6n41-d 7kna-d 5vmj-d 4k66-2 4k66-1 4k62-1 5vmg-d 5vmc-d 6ona-d 4cqw-d 4k64-4 1jsi-2 3zpb-1 4kpq-d 6ns9-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: HEMAGGLUTININ

B: HEMAGGLUTININ

C: HEMAGGLUTININ

hetero molecules

172 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.168, 123.678, 222.163
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

HEMAGGLUTININ

Mass: 57164.238 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-506 / Source method: isolated from a natural source
Source: (natural)

INFLUENZA A VIRUS (A/SINGAPORE/1/1957(H2N2))
References: UniProt: B4UR26, UniProt: Q67333*PLUS

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...

Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2NCC/3=O][Aad21122h-2a_2-6_5NCC/3=O]/1-2-1-3/a3-b1_b4-c1_c6-d2	WURCS	PDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H₂O

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.37 Å³/Da / Density % sol: 63.2 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 74378 / % possible obs: 99.4 % / Observed criterion σ(I): 3.5 / Redundancy: 6.8 % / B_iso Wilson estimate: 62.4 Å² / R_merge(I) obs: 0.11

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→8 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 32.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2964	3742	5 %
R_work	0.2388	-	-
obs	0.2417	74377	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 76.143 Å² / k_sol: 0.379 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.612 Å²	0 Å²	0 Å²
2-	-	2.407 Å²	0 Å²
3-	-	-	0.205 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11251	0	57	348	11656

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	11596
X-RAY DIFFRACTION	f_angle_d	1.326	15674
X-RAY DIFFRACTION	f_dihedral_angle_d	18.857	4223
X-RAY DIFFRACTION	f_chiral_restr	0.084	1694
X-RAY DIFFRACTION	f_plane_restr	0.006	2030

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.5307	0.5043	126	0.4344	2372	X-RAY DIFFRACTION	93
2.5307-2.5629	0.4163	129	0.3894	2597	X-RAY DIFFRACTION	100
2.5629-2.5968	0.3747	147	0.3633	2601	X-RAY DIFFRACTION	100
2.5968-2.6326	0.3974	117	0.3379	2634	X-RAY DIFFRACTION	100
2.6326-2.6705	0.3862	122	0.3402	2609	X-RAY DIFFRACTION	100
2.6705-2.7106	0.4056	149	0.3228	2574	X-RAY DIFFRACTION	100
2.7106-2.7533	0.3703	147	0.3021	2605	X-RAY DIFFRACTION	100
2.7533-2.7987	0.387	139	0.2981	2581	X-RAY DIFFRACTION	100
2.7987-2.8474	0.3662	127	0.2866	2623	X-RAY DIFFRACTION	100
2.8474-2.8996	0.3557	120	0.2816	2617	X-RAY DIFFRACTION	100
2.8996-2.9559	0.3249	144	0.2781	2629	X-RAY DIFFRACTION	100
2.9559-3.0168	0.3493	138	0.2747	2585	X-RAY DIFFRACTION	100
3.0168-3.083	0.3337	157	0.2737	2611	X-RAY DIFFRACTION	100
3.083-3.1555	0.3198	146	0.2612	2581	X-RAY DIFFRACTION	100
3.1555-3.2353	0.298	133	0.2557	2629	X-RAY DIFFRACTION	100
3.2353-3.3239	0.3414	144	0.2593	2624	X-RAY DIFFRACTION	100
3.3239-3.423	0.3421	136	0.2486	2643	X-RAY DIFFRACTION	100
3.423-3.5351	0.3103	130	0.2369	2616	X-RAY DIFFRACTION	100
3.5351-3.6635	0.258	167	0.2179	2611	X-RAY DIFFRACTION	100
3.6635-3.8129	0.2746	140	0.2046	2630	X-RAY DIFFRACTION	100
3.8129-3.9901	0.2503	129	0.2046	2653	X-RAY DIFFRACTION	100
3.9901-4.2056	0.2603	131	0.1874	2649	X-RAY DIFFRACTION	100
4.2056-4.4768	0.2549	136	0.184	2646	X-RAY DIFFRACTION	100
4.4768-4.835	0.195	161	0.1684	2617	X-RAY DIFFRACTION	100
4.835-5.3449	0.2292	144	0.177	2684	X-RAY DIFFRACTION	100
5.3449-6.173	0.24	146	0.1929	2698	X-RAY DIFFRACTION	100
6.173-7.9999	0.2873	137	0.2212	2716	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0856	0.1362	-0.3217	0.3168	-0.6818	1.7667	0.0779	-0.2315	-0.0193	0.0424	-0.1067	0.07	-0.0384	0.0739	0.0179	0.1553	-0.0328	-0.0022	0.4569	0.0963	0.1595	-4.2014	2.856	14.4299
2	0.3067	-0.5857	0.9475	0.7295	-1.4138	3.5175	0.092	0.0566	0.0465	0.0265	-0.0837	-0.003	0.1164	0.2008	-0.0241	0.3038	-0.0272	-0.0517	0.28	0.0485	0.3079	16.0413	-2.144	10.1559
3	0.3581	-0.0347	0.4529	0.7173	-1.2048	2.8677	0.1921	-0.0211	-0.1808	-0.1098	-0.0068	-0.0995	0.4954	-0.1422	-0.1645	0.4955	-0.0998	-0.1529	0.2404	0.0923	0.344	0.8034	-14.704	3.3258
4	0.5747	-0.3359	0.668	0.0771	-0.0716	0.9923	-0.0284	-0.1759	0.0217	0.0032	0.0866	0.1058	-0.2729	-0.3337	-0.0249	0.3408	0.1472	-0.0118	0.3132	0.0012	0.3519	-16.2416	30.4297	-27.5227
5	-0.1173	0.2174	-0.1914	0.3911	-0.5726	1.465	0.002	-0.058	-0.0258	0.0002	-0.0722	-0.0542	-0.1513	0.1776	0.0814	0.2807	0.0182	-0.0088	0.3294	0.0206	0.2924	16.2168	22.5042	-35.4898
6	0.115	0.2083	0.5168	0.5362	-0.2024	2.0402	-0.0327	-0.0263	0.0487	0.0165	0.0043	0.0261	0.2453	-0.2139	-0.0037	0.2901	-0.0184	-0.0386	0.2729	0.0061	0.273	-9.3281	0.7719	-42.9718

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 330:487
2	X-RAY DIFFRACTION	2	CHAIN B AND RESID 330:492
3	X-RAY DIFFRACTION	3	CHAIN C AND RESID 330:478
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 9:323
5	X-RAY DIFFRACTION	5	CHAIN B AND RESID 5:323
6	X-RAY DIFFRACTION	6	CHAIN C AND RESID 7:323

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