[English] 日本語
Yorodumi
- PDB-6idd: Crystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6idd
TitleCrystal structure of H7 hemagglutinin mutant SH1-AVPL ( S138A, G186V, T221P, Q226L) from the influenza virus A/Shanghai/1/2013 (H7N9)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / H7N9 / Hemagglutinin
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.383 Å
AuthorsGao, G.F. / Xu, Y. / Qi, J.X.
CitationJournal: Cell Rep / Year: 2019
Title: Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin.
Authors: Xu, Y. / Peng, R. / Zhang, W. / Qi, J. / Song, H. / Liu, S. / Wang, H. / Wang, M. / Xiao, H. / Fu, L. / Fan, Z. / Bi, Y. / Yan, J. / Shi, Y. / Gao, G.F.
History
DepositionSep 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: Hemagglutinin
C: Hemagglutinin
E: Hemagglutinin
G: Hemagglutinin
I: Hemagglutinin
K: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,73915
Polymers332,7486
Non-polymers1,9919
Water8,629479
1
A: Hemagglutinin
E: Hemagglutinin
G: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,4808
Polymers166,3743
Non-polymers1,1065
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-43 kcal/mol
Surface area57290 Å2
MethodPISA
2
C: Hemagglutinin
I: Hemagglutinin
K: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2597
Polymers166,3743
Non-polymers8854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-39 kcal/mol
Surface area57270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.181, 226.274, 116.780
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Hemagglutinin


Mass: 55457.949 Da / Num. of mol.: 6 / Mutation: S165N,N267D,H274Y,N392T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/MH01/2013(H7N9))
Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A088BEK2
#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.: 9
Source method: isolated from a genetically manipulated 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium HEPES pH 7.5, 14% w/v PEG 4000, 7% v/v 2-Propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 150579 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 11.37
Reflection shellResolution: 2.38→2.47 Å / Rmerge(I) obs: 0.864 / Num. unique obs: 13391 / Rsym value: 0.864

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KOL

4kol


Resolution: 2.383→40.549 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 7454 4.96 %
Rwork0.2526 --
obs0.254 150368 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.383→40.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22786 0 0 479 23265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223250
X-RAY DIFFRACTIONf_angle_d0.45831439
X-RAY DIFFRACTIONf_dihedral_angle_d17.2238671
X-RAY DIFFRACTIONf_chiral_restr0.043405
X-RAY DIFFRACTIONf_plane_restr0.0034156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.383-2.40990.40021740.34633423X-RAY DIFFRACTION71
2.4099-2.43830.41132350.35754598X-RAY DIFFRACTION94
2.4383-2.4680.36862440.35064625X-RAY DIFFRACTION96
2.468-2.49930.38462420.35024788X-RAY DIFFRACTION98
2.4993-2.53210.37812560.34914768X-RAY DIFFRACTION99
2.5321-2.56680.36352550.34234849X-RAY DIFFRACTION99
2.5668-2.60350.38082660.34264887X-RAY DIFFRACTION100
2.6035-2.64230.43542660.34474774X-RAY DIFFRACTION100
2.6423-2.68360.37682460.33074888X-RAY DIFFRACTION100
2.6836-2.72760.3892430.33334816X-RAY DIFFRACTION100
2.7276-2.77460.39582490.32764891X-RAY DIFFRACTION100
2.7746-2.82510.33722450.32274783X-RAY DIFFRACTION100
2.8251-2.87940.31992550.30954897X-RAY DIFFRACTION100
2.8794-2.93820.36422360.31184843X-RAY DIFFRACTION100
2.9382-3.0020.35942400.30634878X-RAY DIFFRACTION99
3.002-3.07180.32692770.28514801X-RAY DIFFRACTION99
3.0718-3.14860.32982620.29184856X-RAY DIFFRACTION99
3.1486-3.23370.30922640.29294816X-RAY DIFFRACTION99
3.2337-3.32880.3342490.29394841X-RAY DIFFRACTION99
3.3288-3.43620.28392850.27864826X-RAY DIFFRACTION99
3.4362-3.5590.29352640.2664821X-RAY DIFFRACTION99
3.559-3.70140.29612370.24694791X-RAY DIFFRACTION99
3.7014-3.86970.28092200.2374868X-RAY DIFFRACTION99
3.8697-4.07360.24272430.21834835X-RAY DIFFRACTION99
4.0736-4.32850.22952530.20464840X-RAY DIFFRACTION99
4.3285-4.66230.21982600.19054827X-RAY DIFFRACTION98
4.6623-5.13060.20352530.19354773X-RAY DIFFRACTION98
5.1306-5.87110.20842400.20124809X-RAY DIFFRACTION98
5.8711-7.38970.23852310.21364815X-RAY DIFFRACTION98
7.3897-40.5490.20682640.19244687X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 148.6315 Å / Origin y: 6.2791 Å / Origin z: 133.4352 Å
111213212223313233
T0.2769 Å20.0269 Å2-0.0011 Å2-0.3274 Å20.0186 Å2--0.3736 Å2
L0.1679 °20.0281 °2-0.042 °2-0.448 °20.1227 °2--0.2367 °2
S-0.0128 Å °0.0041 Å °0.0204 Å °0.0427 Å °-0.0008 Å °0.0225 Å °-0.0151 Å °-0.0031 Å °0.0196 Å °
Refinement TLS groupSelection details: all

+
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