[English] 日本語
Yorodumi
- PDB-6tva: Crystal structure of the haemagglutinin from a transmissible H10N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tva
TitleCrystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with avian receptor analogue, 3'-SLN
Components(Haemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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 / metal ion binding
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhang, J. / Xiong, X. / Purkiss, A. / Walker, P. / Gamblin, S. / Skehel, J.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell Host Microbe / Year: 2020
Title: Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals.
Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / ...Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / Xiong, X. / Peng, W. / Bodewes, R. / van der Vries, E. / Osterhaus, A.D.M.E. / Paulson, J.C. / Skehel, J.J. / Fouchier, R.A.M.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haemagglutinin HA1
B: Haemagglutinin HA2
C: Haemagglutinin HA1
D: Haemagglutinin HA2
E: Haemagglutinin HA1
F: Haemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,06315
Polymers164,0236
Non-polymers4,0419
Water21,2941182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37210 Å2
ΔGint-133 kcal/mol
Surface area57540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 214.960, 77.310
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Haemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Haemagglutinin HA1


Mass: 34914.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: A0A0A7HR51
#2: Protein Haemagglutinin HA2


Mass: 19759.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: A0A0A7HR51

-
Sugars , 3 types, 9 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 5 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 1 types, 1182 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 26%-31% PEG600,0.1M HEPES pH 7.5 or 0.1 M tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→53.74 Å / Num. obs: 211775 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.117 / Net I/σ(I): 9.6
Reflection shellResolution: 1.74→1.77 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10548 / CC1/2: 0.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D00
Resolution: 1.74→53.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 10645 5 %RANDOM
Rwork0.2009 201066 --
obs0.2016 211711 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.64 Å2 / Biso mean: 32.8096 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.14 Å2
2--0.07 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.74→53.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11383 0 269 1182 12834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911910
X-RAY DIFFRACTIONr_bond_other_d00.0210511
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.95816158
X-RAY DIFFRACTIONr_angle_other_deg3.826324510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3351470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62624.697545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.948151959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.161565
X-RAY DIFFRACTIONr_chiral_restr0.060.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213245
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022340
X-RAY DIFFRACTIONr_mcbond_it1.3743.0075898
X-RAY DIFFRACTIONr_mcbond_other1.3713.0075897
X-RAY DIFFRACTIONr_mcangle_it2.1734.5087362
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 774 -
Rwork0.34 14886 -
all-15660 -
obs--99.94 %

+
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