[English] 日本語
Yorodumi
- PDB-3qqo: Crystal structure of HA2 R106H mutant of H2 hemagglutinin, acidic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qqo
TitleCrystal structure of HA2 R106H mutant of H2 hemagglutinin, acidic pH form
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion 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 / 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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin.
Authors: Xu, R. / Wilson, I.A.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5379
Polymers169,8736
Non-polymers6643
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32120 Å2
ΔGint-166 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.999, 240.115, 70.332
Angle α, β, γ (deg.)90.00, 116.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hemagglutinin /


Mass: 36504.227 Da / Num. of mol.: 3 / Fragment: HA1 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C7S226
#2: Protein Hemagglutinin /


Mass: 20120.248 Da / Num. of mol.: 3 / Fragment: HA2 chain ectodomain / Mutation: R106H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C7S226
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 16% PEG 3000, 0.1M citric acid, pH 5.3, vapor diffusion, sitting drop, temperature 295.5K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2009
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 14.44 / Number: 133153 / Rmerge(I) obs: 0.078 / Χ2: 1.04 / D res high: 2.9 Å / D res low: 45 Å / Num. obs: 39294 / % possible obs: 88.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.244599.610.0480.9743.6
4.966.2410010.0651.0423.7
4.334.9610010.071.0033.6
3.944.3310010.081.0353.6
3.653.9499.610.1041.0843.5
3.443.6598.410.1341.063.3
3.273.4492.510.1811.0693.3
3.123.2781.910.2171.0793.1
33.1264.410.2621.0232.9
2.9346.910.3220.9982.7
ReflectionResolution: 2.9→45 Å / Num. obs: 39294 / % possible obs: 88.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.9-32.70.32246.9
3-3.122.90.26264.4
3.12-3.273.10.21781.9
3.27-3.443.30.18192.5
3.44-3.653.30.13498.4
3.65-3.943.50.10499.6
3.94-4.333.60.08100
4.33-4.963.60.07100
4.96-6.243.70.065100
6.24-453.60.04899.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.75 Å49.44 Å
Translation2.75 Å49.44 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.437 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.43 / σ(F): 1.91 / Phase error: 34.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 1991 5.08 %
Rwork0.2217 --
obs0.2252 39216 88.12 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.863 Å2 / ksol: 0.267 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.8786 Å2-0 Å29.652 Å2
2---27.5348 Å2-0 Å2
3---13.1256 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11736 0 42 56 11834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412105
X-RAY DIFFRACTIONf_angle_d0.80716359
X-RAY DIFFRACTIONf_dihedral_angle_d14.5724482
X-RAY DIFFRACTIONf_chiral_restr0.0551743
X-RAY DIFFRACTIONf_plane_restr0.0032133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00370.46891100.35951944X-RAY DIFFRACTION46
3.0037-3.12390.40641280.3012699X-RAY DIFFRACTION64
3.1239-3.2660.3541890.2923434X-RAY DIFFRACTION81
3.266-3.43810.35462250.28553867X-RAY DIFFRACTION92
3.4381-3.65340.32342250.26374135X-RAY DIFFRACTION98
3.6534-3.93540.32372150.23524224X-RAY DIFFRACTION100
3.9354-4.33110.27492240.20124210X-RAY DIFFRACTION100
4.3311-4.9570.23932290.1744223X-RAY DIFFRACTION100
4.957-6.24240.26872350.194234X-RAY DIFFRACTION100
6.2424-43.44170.2492110.2094255X-RAY DIFFRACTION99

+
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