[English] 日本語
Yorodumi
- PDB-8tj9: CRYSTAL STRUCTURE OF THE A/Michigan/15/2014(H3N2) INFLUENZA VIRUS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tj9
TitleCRYSTAL STRUCTURE OF THE A/Michigan/15/2014(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 / 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 / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 16, 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)60,61621
Polymers55,9202
Non-polymers4,69619
Water8,395466
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)181,84963
Polymers167,7596
Non-polymers14,08957
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 area54710 Å2
ΔGint-95 kcal/mol
Surface area59410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.591, 100.591, 394.890
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 chain


Mass: 35923.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Michigan/15/2014(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3
#2: Protein Hemagglutinin HA2 chain


Mass: 19996.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Michigan/15/2014(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3

-
Sugars , 3 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.: 3
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 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
#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.: 3
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 , 6 types, 478 molecules

#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% PEG-400, 0.2 M Lithium sulfate, and 0.1M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→42.53 Å / Num. obs: 61131 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 42.3
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 5474 / CC1/2: 0.925 / Rpim(I) all: 0.23 / Rsym value: 0.99

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.53 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 3135 5.13 %
Rwork0.1606 --
obs0.1619 61121 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 306 466 4642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094246
X-RAY DIFFRACTIONf_angle_d0.9955725
X-RAY DIFFRACTIONf_dihedral_angle_d9.51671
X-RAY DIFFRACTIONf_chiral_restr0.066662
X-RAY DIFFRACTIONf_plane_restr0.009715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.25321510.22772609X-RAY DIFFRACTION100
1.93-1.960.19971520.18932565X-RAY DIFFRACTION100
1.96-20.21821370.17722623X-RAY DIFFRACTION100
2-2.030.20911350.17182585X-RAY DIFFRACTION100
2.03-2.070.22621460.17522610X-RAY DIFFRACTION100
2.07-2.110.19371460.17292614X-RAY DIFFRACTION100
2.11-2.160.21251530.16742587X-RAY DIFFRACTION100
2.16-2.210.21941400.16272609X-RAY DIFFRACTION100
2.21-2.260.22371360.15722608X-RAY DIFFRACTION100
2.26-2.330.23751320.16912652X-RAY DIFFRACTION100
2.33-2.390.181300.15752627X-RAY DIFFRACTION100
2.39-2.470.23081300.16382624X-RAY DIFFRACTION100
2.47-2.560.18291670.16962597X-RAY DIFFRACTION100
2.56-2.660.20971280.16622656X-RAY DIFFRACTION100
2.66-2.780.19991550.17742604X-RAY DIFFRACTION100
2.78-2.930.18861530.16752637X-RAY DIFFRACTION100
2.93-3.110.16411450.15792633X-RAY DIFFRACTION100
3.11-3.350.19571640.16572649X-RAY DIFFRACTION100
3.35-3.690.15981180.14952681X-RAY DIFFRACTION100
3.69-4.230.14881250.1372690X-RAY DIFFRACTION100
4.23-5.320.15971490.13582711X-RAY DIFFRACTION100
5.32-42.530.18791430.17922815X-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)
10.95770.2448-0.42241.25850.42641.96670.00260.1192-0.1870.0689-0.13590.16470.5175-0.47680.09680.2147-0.0186-0.06230.1668-0.00760.2829-58.001513.379419.1753
20.54420.20630.25320.2413-0.60252.90440.0174-0.033-0.1074-0.14940.08980.0360.448-0.1475-0.11560.2682-0.0318-0.06470.15620.00480.2849-54.93998.415538.1053
30.5787-0.28420.15830.73320.0692.57290.0333-0.2558-0.32040.21510.06180.02830.55380.214-0.09370.35840.039-0.09940.27720.08340.3218-42.492.452671.0843
41.215-0.0556-0.02891.11150.06711.4856-0.0546-0.5744-0.12520.51170.1519-0.08610.24780.1026-0.12230.50710.0894-0.10660.50610.08480.2586-40.800510.058390.0157
51.5110.53480.70763.1171-1.25771.1055-0.0811-0.5780.09670.80880.15630.0341-0.2426-0.0583-0.1220.64120.0677-0.0570.5039-0.03420.272-39.277424.251693.704
61.5719-0.27030.32481.2188-0.01181.4048-0.0437-0.5981-0.13610.43440.08430.03790.0403-0.0512-0.06270.48680.0286-0.06370.41770.0560.2278-44.930616.027390.0047
70.64740.02690.57920.43010.24791.82520.0743-0.1109-0.0450.26560.0791-0.12480.11110.1745-0.15940.34310.0283-0.09960.33260.07280.2879-40.20039.829176.0368
81.57090.0742-0.26181.6186-0.4531.92780.1117-0.1086-0.23650.02560.0819-0.11360.43150.0335-0.19990.26490.028-0.0740.19250.02960.2923-48.52877.308751.9221
90.94430.05890.18450.4449-0.14394.0380.0712-0.0899-0.0910.0030.01190.02530.5312-0.3823-0.02070.1678-0.0395-0.02580.10680.01940.2192-54.196313.385438.4744
101.1507-0.1609-0.54210.5396-0.0971.45380.02570.1695-0.0128-0.18390.0447-0.07530.417-0.198-0.06160.2863-0.0177-0.05170.131-0.02980.2535-53.587311.229110.2171
110.40560.13710.75971.42832.62328.93420.05560.0059-0.04350.04260.0108-0.0820.55270.2918-0.11080.21290.0416-0.05130.1437-0.01310.2598-44.386511.993620.7288
120.4923-0.56110.32941.69811.06132.1388-0.0207-0.159-0.17490.22630.10460.01630.280.214-0.07670.2697-0.0193-0.05490.23850.05730.2651-48.780216.467660.5444
130.2653-0.0102-0.09850.21880.43952.61340.04890.0034-0.0407-0.01950.02760.0139-0.0638-0.0673-0.07030.15630.0029-0.00750.10730.00240.2322-51.596822.700630.9259
141.50870.2002-0.56052.0662-0.05241.5171-0.01890.2496-0.1766-0.28410.041-0.07150.16040.0636-0.03350.27220.01050.0030.217-0.05340.2226-46.708715.871-6.5975
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 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 89 )
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 214 )
6X-RAY DIFFRACTION6chain 'A' and (resid 215 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 275 )
8X-RAY DIFFRACTION8chain 'A' and (resid 276 through 300 )
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 325 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 30 )
11X-RAY DIFFRACTION11chain 'B' and (resid 31 through 55 )
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 75 )
13X-RAY DIFFRACTION13chain 'B' and (resid 76 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 173 )

+
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