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

ID or keywords:

Entry

Database: PDB / ID: 2wrb

Title

the structure of influenza H2 human singapore hemagglutinin with avian receptor

Components

HEMAGGLUTININ

Keywords

VIRAL PROTEIN / GLYCOPROTEIN / LIPOPROTEIN / ENVELOPE PROTEIN

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: 3.1 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	Sep 1, 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 1.3	Jul 1, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_validate_close_contact / struct_conn / struct_conn_type Item: _chem_comp.type / _pdbx_database_status.status_code_sf
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5	Oct 16, 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

-
Download

PDBx/mmCIF format	2wrb.cif.gz	564.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2wrb.ent.gz	470.6 KB	Display	PDB format
PDBx/mmJSON format	2wrb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/2wrb ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wrb	HTTPS FTP

-
Related structure data

Related structure data	2wr0C 2wr1C 2wr2C 2wr3C 2wr4C 2wr5C 2wr7C 2wrcC 2wrdC 2wreC 2wrfC 2wrgC 2wrhC C: citing same article (ref.)
Similar structure data	1jsm-2 6mya-1 4edb-d 3htp-1 6ona-d 1rvz-2 6d8w-2 1ru7-2 6mya-2 6lks-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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) #113 - May 2009 Influenza Neuraminidase similarity (1) #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)

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)
#113 - May 2009
Influenza Neuraminidase
similarity (1)
#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)	83.359, 126.303, 220.956
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 9:324 OR RESSEQ 330:487 )
2	1	1	CHAIN B AND (RESSEQ 9:324 OR RESSEQ 330:487 )
3	1	1	CHAIN C AND (RESSEQ 9:324 OR RESSEQ 330:478 )

#1: Protein

HEMAGGLUTININ

Mass: 57164.238 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural)

INFLUENZA A VIRUS / References: UniProt: Q67333*PLUS

#2: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

Has protein modification

Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 66.94 % / Description: NONE

-
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: 3.1→30 Å / Num. obs: 40025 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / B_iso Wilson estimate: 71.13 Å² / R_merge(I) obs: 0.14

-
Processing

Software

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

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 3.1→7.999 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 30.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2964	2008	5 %
R_work	0.2528	-	-
obs	0.2549	40025	98.93 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.099 Å² / k_sol: 0.327 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1502 Å²	0 Å²	0 Å²
2-	-	0.8931 Å²	0 Å²
3-	-	-	1.2571 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→7.999 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11059	0	21	0	11080

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11557
X-RAY DIFFRACTION	f_angle_d	1.142	15616
X-RAY DIFFRACTION	f_dihedral_angle_d	17.462	4195
X-RAY DIFFRACTION	f_chiral_restr	0.073	1679
X-RAY DIFFRACTION	f_plane_restr	0.006	2029

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3736	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3736	X-RAY DIFFRACTION	POSITIONAL	0.045
1	3	C	3667	X-RAY DIFFRACTION	POSITIONAL	0.041

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 (%)
3.1-3.1728	0.3917	147	0.3658	2694	X-RAY DIFFRACTION	100
3.1728-3.253	0.3489	161	0.3413	2671	X-RAY DIFFRACTION	100
3.253-3.3419	0.3897	142	0.3207	2734	X-RAY DIFFRACTION	100
3.3419-3.4415	0.3219	138	0.3112	2714	X-RAY DIFFRACTION	99
3.4415-3.554	0.3435	144	0.3044	2673	X-RAY DIFFRACTION	99
3.554-3.6829	0.3595	161	0.3303	2701	X-RAY DIFFRACTION	99
3.6829-3.8328	0.3275	141	0.2902	2705	X-RAY DIFFRACTION	99
3.8328-4.0105	0.3298	140	0.2964	2689	X-RAY DIFFRACTION	98
4.0105-4.2266	0.2702	137	0.2374	2709	X-RAY DIFFRACTION	98
4.2266-4.4983	0.2019	140	0.2075	2704	X-RAY DIFFRACTION	99
4.4983-4.8569	0.2237	153	0.1741	2731	X-RAY DIFFRACTION	99
4.8569-5.3666	0.2475	127	0.1879	2733	X-RAY DIFFRACTION	98
5.3666-6.1921	0.2888	137	0.2033	2746	X-RAY DIFFRACTION	98
6.1921-7.9987	0.2704	140	0.2244	2813	X-RAY DIFFRACTION	99

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	1.0529	-0.0688	0.2083	0.5008	-0.6487	1.7934	0.118	0.8569	-0.0316	-0.1602	-0.0113	-0.1774	0.1766	0.7984	-0.0788	0.2216	0.1654	0.0212	0.9609	-0.0869	0.285	4.559	-2.6777	-14.9379
2	0.5095	0.8457	1.1969	1.3067	1.2475	2.9506	0.1014	-0.1451	0.0828	-0.1752	-0.173	0.1371	-0.0401	-0.3983	0.0061	0.2976	0.0663	-0.0958	0.4213	-0.0964	0.3543	-16.3502	-2.513	-11.6376
3	1.1004	-0.0339	0.2151	0.4987	0.6974	4.8804	0.1824	0.3641	-0.3709	0.1459	-0.0841	-0.0671	1.524	0.0779	-0.0272	0.7175	0.1113	-0.0884	0.2385	-0.1614	0.3425	-5.2097	-18.0021	-4.3681
4	0.2761	0.7306	-0.031	0.9704	1.1633	2.3507	-0.142	0.8303	-0.1178	-0.3222	0.3265	-0.2641	-0.0811	1.6072	-0.1907	0.353	0.189	0.0248	1.5025	-0.2049	0.446	16.0126	-1.1245	-5.6808
5	-0.1828	0.5185	0.6569	0.9489	1.5735	5.0386	-0.2536	0.0184	-0.0705	-0.5163	-0.101	0.4812	-0.5728	0.373	0.2357	0.5489	0.1762	-0.2186	0.3944	-0.0357	0.3145	-17.017	9.7143	-6.5767
6	0.8001	0.4932	0.5605	-2.11	0.3049	4.4337	0.2968	0.2933	-0.534	0.2085	-0.1397	0.0326	2.339	-0.0223	-0.271	1.1767	-0.1023	-0.1419	0.18	-0.1208	0.4251	-9.1616	-20.489	7.1986
7	-2.0131	0.4277	-2.0156	0.8954	0.3964	2.8672	0.1567	0.0496	-0.3732	-0.284	0.2542	-0.7317	-0.2675	1.4238	-0.3593	0.3623	-0.4984	-0.0166	1.1028	0.0605	0.7312	24.8793	22.5644	27.9133
8	1.5095	0.034	0.6244	-1.1622	-1.7367	2.0497	0.0439	0.2967	-0.0349	0.6511	-0.1	-0.2142	-0.5243	-0.0939	0.0632	0.5285	0.031	-0.0263	0.2153	-0.0652	0.4338	-14.3461	24.9298	35.9249
9	1.0207	-0.6415	0.1525	1.2857	2.4399	1.233	0.0941	-0.0285	-0.0394	0.3635	-0.1818	0.2821	0.4226	0.3114	0.128	0.5519	0.0771	-0.0203	0.315	0.0559	0.4489	6.0629	-7.781	45.8464
10	0.419	0.063	0.0789	1.5387	0.7525	2.4529	-0.0866	-0.0003	0.3051	0.0183	0.0692	-0.2313	-0.9029	1.0594	-0.0129	0.6865	-0.5985	-0.1725	0.7164	0.087	0.5618	23.3767	31.3447	45.3882
11	1.2551	0.0317	0.3244	-0.633	-0.1159	2.7405	-0.2099	-0.0679	0.0608	0.2617	0.1348	-0.0841	-0.6683	-0.0221	0.0866	0.6355	-0.0672	-0.0839	0.1086	-0.0298	0.3947	-8.4663	27.3723	54.4706
12	0.3505	0.0662	1.7657	3.5937	0.5701	2.4059	-0.0615	0.1265	0.0162	0.7178	0.0061	-0.4943	0.0494	0.7791	0.0669	0.4066	-0.0108	-0.1124	0.4381	0.0597	0.3703	13.4444	3.4031	60.1562
13	1.3505	1.2592	0.3004	1.4728	1.9611	2.7612	0.2678	1.0885	-0.0955	-1.1041	0.0421	-0.5941	-0.8832	1.5782	-0.3549	-0.0554	-0.331	-0.078	0.6193	0.0695	0.3387	17.988	15.4381	15.7465
14	0.1751	-0.3925	-0.007	1.3799	1.0519	1.8168	0.0708	0.102	0.0133	-0.1256	-0.2382	-0.0307	-0.7244	-0.2883	0.1775	0.283	-0.0443	-0.1157	0.1998	-0.0301	0.2587	-14.4093	16.2825	22.8739
15	0.2535	0.2217	0.8433	1.1492	-0.3921	3.2117	0.1615	0.082	-0.0186	-0.0736	-0.1658	-0.0725	1.0163	0.2229	0.0328	0.3484	0.115	0.029	0.1951	-0.0035	0.2832	3.6014	-10.1954	30.5834

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 330:492
2	X-RAY DIFFRACTION	2	CHAIN B AND RESID 330:492
3	X-RAY DIFFRACTION	3	CHAIN C AND RESID 330:492
4	X-RAY DIFFRACTION	4	CHAIN A AND RESID 5:49
5	X-RAY DIFFRACTION	5	CHAIN B AND RESID 5:49
6	X-RAY DIFFRACTION	6	CHAIN C AND RESID 5:49
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 50:113
8	X-RAY DIFFRACTION	8	CHAIN B AND RESID 50:113
9	X-RAY DIFFRACTION	9	CHAIN C AND RESID 50:113
10	X-RAY DIFFRACTION	10	CHAIN A AND RESID 114-240
11	X-RAY DIFFRACTION	11	CHAIN B AND RESID 114-240
12	X-RAY DIFFRACTION	12	CHAIN C AND RESID 114-240
13	X-RAY DIFFRACTION	13	CHAIN A AND RESID 241-323
14	X-RAY DIFFRACTION	14	CHAIN B AND RESID 241-323
15	X-RAY DIFFRACTION	15	CHAIN C AND RESID 241-323

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi