[English] 日本語
Yorodumi
- PDB-5vjl: Crystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vjl
TitleCrystal structure of H7 hemagglutinin mutant (V186K, K193T, G228S) from the influenza virus A/Shanghai/2/2013 (H7N9) with LSTc
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / mutant / receptor specificity
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 / metal ion binding
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
METHANOL / N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Three mutations switch H7N9 influenza to human-type receptor specificity.
Authors: de Vries, R.P. / Peng, W. / Grant, O.C. / Thompson, A.J. / Zhu, X. / Bouwman, K.M. / de la Pena, A.T.T. / van Breemen, M.J. / Ambepitiya Wickramasinghe, I.N. / de Haan, C.A.M. / Yu, W. / ...Authors: de Vries, R.P. / Peng, W. / Grant, O.C. / Thompson, A.J. / Zhu, X. / Bouwman, K.M. / de la Pena, A.T.T. / van Breemen, M.J. / Ambepitiya Wickramasinghe, I.N. / de Haan, C.A.M. / Yu, W. / McBride, R. / Sanders, R.W. / Woods, R.J. / Verheije, M.H. / Wilson, I.A. / Paulson, J.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Data collection
Revision 1.2Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4527
Polymers56,4472
Non-polymers1,0055
Water55831
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,35621
Polymers169,3416
Non-polymers3,01515
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area35290 Å2
ΔGint-141 kcal/mol
Surface area56450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.375, 116.375, 296.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1


Mass: 35365.891 Da / Num. of mol.: 1 / Mutation: V186K, K193T, G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2


Mass: 21081.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21

-
Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / 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
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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 / 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

-
Non-polymers , 2 types, 32 molecules

#4: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: CH4O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M tri-potassium citrate, 5% (v/v) ethylene glycol and 22% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24049 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rsym value: 0.08 / Net I/σ(I): 28.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1160 / CC1/2: 0.69 / Rpim(I) all: 0.44 / Rsym value: 0.7 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N5J

4n5j


Resolution: 2.597→47.703 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 1229 5.11 %
Rwork0.2176 --
obs0.2206 24028 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.597→47.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 64 31 3852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133901
X-RAY DIFFRACTIONf_angle_d1.7655280
X-RAY DIFFRACTIONf_dihedral_angle_d16.1222304
X-RAY DIFFRACTIONf_chiral_restr0.099577
X-RAY DIFFRACTIONf_plane_restr0.011695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5969-2.70090.36791290.31262442X-RAY DIFFRACTION97
2.7009-2.82380.34381220.29982539X-RAY DIFFRACTION100
2.8238-2.97260.35851450.28672501X-RAY DIFFRACTION100
2.9726-3.15880.36061370.26372523X-RAY DIFFRACTION100
3.1588-3.40270.34861380.26222519X-RAY DIFFRACTION100
3.4027-3.7450.30481310.22262549X-RAY DIFFRACTION100
3.745-4.28660.2351350.19412549X-RAY DIFFRACTION99
4.2866-5.39950.22251530.18372506X-RAY DIFFRACTION98
5.3995-47.71070.27071390.20672671X-RAY DIFFRACTION99
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)
11.61410.151.02551.36621.1045.41590.042-0.0753-0.29780.10820.1284-0.3427-0.02870.3906-0.14260.5026-0.00020.02350.39810.00130.5875-49.135414.67643.8007
27.39931.67080.06443.0983-1.03557.5686-0.45481.2153-0.396-0.81110.48260.45820.6643-0.4569-0.02880.5877-0.0206-0.00670.6301-0.05170.6982-64.71058.1767-26.6528
37.4421.865-2.23173.0932-2.27518.1804-0.0951.14190.5643-0.69130.50550.4346-0.05880.2919-0.59860.7672-0.1818-0.06770.6670.01030.6498-59.356215.6017-32.6574
48.31214.6148-5.56124.1683-2.63699.0139-0.40080.37190.4534-0.12360.56390.6656-0.47420.98330.03270.9563-0.1280.04280.72520.00660.7532-51.10920.6306-28.1359
51.75810.27271.11341.7651-0.20081.9980.00970.16820.0430.1062-0.05480.10440.30960.0807-0.11990.4378-0.04770.06460.4809-0.00910.6104-56.782213.0656-6.5842
63.24840.14711.92612.33660.27849.1126-0.6276-0.4795-0.2720.31610.1152-0.0035-0.42870.5020.29780.5130.07180.01280.66050.02470.5463-46.477823.01922.0884
74.4091-2.75920.53334.1976-2.16421.52690.482-1.53640.81671.6024-1.3452-0.93080.21411.3060.44711.96-0.0722-0.41261.79210.25340.694-45.670121.497950.0023
85.4511-1.04365.17164.4174-2.90345.6743-0.0773-1.6654-0.18050.3239-0.2219-0.25942.14-0.74750.31791.2505-0.00160.01711.16720.21850.6467-53.130915.557144.3007
98.6112-2.5252-0.86257.7408-0.2351.9085-0.56120.6338-0.74440.14950.2997-0.0291-0.2649-1.09620.24020.60890.04790.01330.6045-0.04140.6529-54.05320.72841.3133
102.36290.07960.52181.6765-0.49485.19870.1781-1.2149-0.11730.9914-0.1085-0.2013-0.30890.5460.16340.899-0.0356-0.13610.9340.06180.5189-52.6927.791337.6162
113.09620.0743-0.0821.06612.74317.0401-0.675-0.9177-1.62581.7290.29440.86271.5994-0.429-0.5572.86110.0867-0.08072.31080.44270.5805-57.276216.706967.8212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 237 )
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 298 )
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 325 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 74 )
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 145 )
11X-RAY DIFFRACTION11chain 'B' and (resid 146 through 168 )

+
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