[English] 日本語
Yorodumi
- PDB-4we6: The crystal structure of hemagglutinin HA1 domain from influenza ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4we6
TitleThe crystal structure of hemagglutinin HA1 domain from influenza virus A/Perth/142/2007(H3N2)
ComponentsHemagglutinin HA1 chain
KeywordsVIRAL PROTEIN / hemagglutinin / HA1 / H3N2 / influenza virus
Function / homology
Function and homology information


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 / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.904 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,61710
Polymers62,3642
Non-polymers1,2538
Water10,449580
1
A: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8095
Polymers31,1821
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8095
Polymers31,1821
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.472, 50.567, 182.256
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein Hemagglutinin HA1 chain


Mass: 31182.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Perth/142/2007(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G8HJ45, UniProt: B2VNP1*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5 / Details: 0.1M MgCl2, 0.1 Tris-HCl, pH8.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 56707 / Num. obs: 56707 / % possible obs: 98.2 % / Redundancy: 3.4 % / Net I/σ(I): 12.8

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 1.904→44.216 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3023 5.06 %
Rwork0.1695 --
obs0.1711 56707 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→44.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 80 580 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024486
X-RAY DIFFRACTIONf_angle_d1.6836074
X-RAY DIFFRACTIONf_dihedral_angle_d12.811656
X-RAY DIFFRACTIONf_chiral_restr0.135662
X-RAY DIFFRACTIONf_plane_restr0.009784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9041-1.93380.30581290.26352482X-RAY DIFFRACTION93
1.9338-1.96560.27961410.22632513X-RAY DIFFRACTION99
1.9656-1.99940.22891440.20952624X-RAY DIFFRACTION99
1.9994-2.03580.23961400.18832604X-RAY DIFFRACTION99
2.0358-2.0750.23741410.17962581X-RAY DIFFRACTION100
2.075-2.11730.21861420.18252669X-RAY DIFFRACTION100
2.1173-2.16330.20231360.1742526X-RAY DIFFRACTION99
2.1633-2.21370.18691400.16042646X-RAY DIFFRACTION100
2.2137-2.2690.21371400.16762605X-RAY DIFFRACTION100
2.269-2.33040.1931200.16062645X-RAY DIFFRACTION100
2.3304-2.39890.18641400.16682639X-RAY DIFFRACTION100
2.3989-2.47640.21281420.17342590X-RAY DIFFRACTION100
2.4764-2.56490.20151450.16642621X-RAY DIFFRACTION100
2.5649-2.66750.19141470.15742652X-RAY DIFFRACTION99
2.6675-2.78890.20951230.15772569X-RAY DIFFRACTION99
2.7889-2.93590.20621390.16182575X-RAY DIFFRACTION99
2.9359-3.11980.19611340.1642620X-RAY DIFFRACTION98
3.1198-3.36070.20871330.15892571X-RAY DIFFRACTION97
3.3607-3.69870.16481350.15232514X-RAY DIFFRACTION95
3.6987-4.23350.17111480.14892533X-RAY DIFFRACTION95
4.2335-5.33240.18671360.15422385X-RAY DIFFRACTION90
5.3324-44.22770.21691280.20622532X-RAY DIFFRACTION91
Refinement TLS params.

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

IDL11 (°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)
10.5957-0.54350.6471.2202-1.22622.44730.0097-0.01770.07560.0277-0.03750.0140.21920.0538-0.0255-0.0205-0.01990.01360.05580.00970.069517.0786-16.785359.6331
21.0016-0.91420.56860.7153-0.1132.2178-0.048-0.16310.07140.35010.00920.0214-0.2403-0.3501-0.01180.1272-0.017-0.0270.0962-0.02970.049617.6122-12.535175.2773
30.3434-0.73530.08441.0686-0.66020.6120.1367-0.05110.0379-0.1765-0.0650.12870.0185-0.19940.00850.0169-0.02240.00720.05880.04640.0977.4286-9.305246.3813
40.69350.6281-0.69251.5865-1.21832.59070.04320.0082-0.0425-0.0456-0.05950.0275-0.36780.0665-0.0166-0.11590.0394-0.01040.02470.01130.0643-4.1285-31.347931.4802
50.69520.7484-0.5750.67250.00722.2417-0.03720.1376-0.0703-0.3663-0.009-0.00290.1963-0.3252-0.03420.0970.00960.01110.1085-0.010.0673-3.5471-35.587215.8347
60.21940.5654-0.05960.9222-0.56680.80060.14040.0315-0.03370.1688-0.05620.1439-0.057-0.17950.00040.04690.01640.00140.07760.04650.1122-13.7939-38.843244.7235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 135 )
2X-RAY DIFFRACTION2chain 'A' and (resid 136 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 270 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 135 )
5X-RAY DIFFRACTION5chain 'B' and (resid 136 through 207 )
6X-RAY DIFFRACTION6chain 'B' and (resid 208 through 270 )

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more