[English] 日本語
Yorodumi
- PDB-8tjb: CRYSTAL STRUCTURE OF THE A/Texas/73/2017(H3N2) INFLUENZA VIRUS HE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tjb
TitleCRYSTAL STRUCTURE OF THE A/Texas/73/2017(H3N2) INFLUENZA VIRUS HEMAGGLUTININ WITH HUMAN RECEPTOR ANALOG 6'-SLNLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / INFLUENZA / HEMAGGLUTININ / RECEPTOR
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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWu, N.C. / Zhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Host Microbe / Year: 2024
Title: Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site.
Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / ...Authors: Thompson, A.J. / Wu, N.C. / Canales, A. / Kikuchi, C. / Zhu, X. / de Toro, B.F. / Canada, F.J. / Worth, C. / Wang, S. / McBride, R. / Peng, W. / Nycholat, C.M. / Jimenez-Barbero, J. / Wilson, I.A. / Paulson, J.C.
History
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 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 HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4239
Polymers56,1082
Non-polymers4,3157
Water2,702150
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,26927
Polymers168,3246
Non-polymers12,94521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area49090 Å2
ΔGint59 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.240, 100.240, 391.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

21B-265-

HOH

-
Components

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

#1: Protein Hemagglutinin HA1 chain


Mass: 35981.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Texas/73/2017(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1W6AW68
#2: Protein Hemagglutinin HA2 chain


Mass: 20126.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Texas/73/2017(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A1W6AW68

-
Sugars , 5 types, 7 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1039.937 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-2-3/a4-b1_b3-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#7: 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.: 2
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

-
Non-polymers , 1 types, 150 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 30% 1,2-propanediol, 20% PEG-400, and 0.1M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.45→43.14 Å / Num. obs: 28518 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rpim(I) all: 0.04 / Rsym value: 0.1 / Net I/σ(I): 30
Reflection shellResolution: 2.45→2.55 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3105 / CC1/2: 0.867 / Rpim(I) all: 0.41 / Rsym value: 1

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.14 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1483 5.21 %
Rwork0.2384 --
obs0.2424 28464 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 288 150 4313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034245
X-RAY DIFFRACTIONf_angle_d0.6075745
X-RAY DIFFRACTIONf_dihedral_angle_d11.53693
X-RAY DIFFRACTIONf_chiral_restr0.046687
X-RAY DIFFRACTIONf_plane_restr0.003716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.530.36551220.35342395X-RAY DIFFRACTION100
2.53-2.620.411480.32892401X-RAY DIFFRACTION100
2.62-2.720.33881460.32592406X-RAY DIFFRACTION100
2.72-2.850.36891420.30352425X-RAY DIFFRACTION100
2.85-30.35991120.27992444X-RAY DIFFRACTION99
3-3.180.29361280.26332420X-RAY DIFFRACTION100
3.18-3.430.28291160.24792462X-RAY DIFFRACTION100
3.43-3.770.24671690.21722424X-RAY DIFFRACTION100
3.77-4.320.25211170.20332491X-RAY DIFFRACTION100
4.32-5.440.24551400.20632503X-RAY DIFFRACTION100
5.44-43.140.26881430.23632610X-RAY DIFFRACTION100
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)
11.4541-0.02190.1940.64280.07231.3657-0.0824-0.1778-0.38560.3323-0.16170.0440.7756-0.06440.26590.5723-0.0850.09790.44510.08710.545740.2721-43.2997-18.8751
21.07410.4452-0.45291.34850.43031.75130.02030.1809-0.2762-0.29030.11010.46470.4424-1.0317-0.07280.2943-0.0171-0.07150.44450.01190.512726.1559-37.8233-61.824
32.52490.1594-0.32480.82020.10561.21250.06140.83880.01-0.53050.09710.49380.1243-0.6075-0.07660.5322-0.01-0.20230.76860.0470.571528.9652-31.4922-82.5246
41.17480.39860.36142.57520.85041.7576-0.54210.8170.3197-0.82570.40541.1750.435-1.14910.1840.7785-0.1133-0.25220.9836-0.03460.608922.6119-37.6978-91.2128
52.33780.53420.41491.9579-0.90861.5494-0.07591.07690.1209-1.28020.03950.2755-0.3939-0.26460.10750.8370.0116-0.15821.00620.04430.503432.6735-26.8195-96.4599
62.92250.08460.14071.334-0.54692.0969-0.04010.48980.0402-0.42590.0618-0.25480.20280.10630.07340.6982-0.0098-0.09650.72180.00430.416937.2692-27.9652-89.4074
70.99560.0886-0.07150.46910.30591.6678-0.05380.0741-0.0583-0.16950.10640.19460.0244-0.5191-0.07140.4185-0.0257-0.09590.5490.01730.491629.9997-34.0552-62.3997
80.8332-0.7858-0.50720.92130.14895.8244-0.0294-0.2728-0.26230.0751-0.04030.02411.16320.38230.10010.4683-0.03640.04210.35040.02810.453239.9659-43.0146-30.9577
91.5383-0.0518-0.4191.0213-0.08290.7458-0.0052-0.7562-0.25910.2763-0.06290.25970.3859-0.2684-0.0670.5149-0.01610.07860.64090.09810.435137.7653-40.2382-13.2528
100.77290.0258-0.31431.1066-0.32871.9388-0.1137-0.1251-0.13160.28940.07060.087-0.3107-0.87750.08790.41720.00580.07550.56030.02710.553431.8438-33.6498-15.7784
110.8398-0.19790.21910.8805-0.58050.2524-0.0156-0.39020.6335-0.03590.0860.2254-0.61340.16340.20650.4215-0.0461-0.0090.6744-0.10380.707233.4734-28.3594-52.2031
121.1784-0.0308-1.55030.9043-0.85353.0252-0.02920.0586-0.1435-0.0556-0.00340.06320.322-0.2510.09440.1965-0.0509-0.01120.24250.01630.371945.1515-34.4788-40.0726
131.51630.5403-0.3491.4695-0.03981.12210.1152-0.39720.00510.4526-0.03030.1693-0.037-0.0654-0.13850.75110.01750.11740.89670.02380.507237.2421-31.74936.0912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 153 )
5X-RAY DIFFRACTION5chain 'A' and (resid 154 through 201 )
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 308 )
8X-RAY DIFFRACTION8chain 'A' and (resid 309 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 25 )
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 65 )
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 172 )

+
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