[English] 日本語
Yorodumi
- PDB-4xkf: Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xkf
TitleCrystal structure of hemagglutinin from Taiwan (2013) H6N1 influenza virus in complex with LSTa
Components
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus 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 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
Hemagglutinin HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 Å
AuthorsTzarum, N. / Zhu, X. / Wilson, I.A.
CitationJournal: Cell Host Microbe / Year: 2015
Title: Structure and Receptor Binding of the Hemagglutinin from a Human H6N1 Influenza Virus.
Authors: Tzarum, N. / de Vries, R.P. / Zhu, X. / Yu, W. / McBride, R. / Paulson, J.C. / Wilson, I.A.
History
DepositionJan 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,89113
Polymers173,8896
Non-polymers2,0027
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31310 Å2
ΔGint-136 kcal/mol
Surface area61290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.735, 99.271, 133.437
Angle α, β, γ (deg.)90.000, 126.450, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hemagglutinin HA1 chain


Mass: 37331.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Taiwan/2/2013(H6N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A0J9X268*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 20631.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Taiwan/2/2013(H6N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A0J9X267*PLUS
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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.: 6 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10mM NiCl2, 0.1M Tris pH 8.5, 20% (w/v) MPEG 2000 and 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.446→50 Å / Num. obs: 71296 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.063 / Rrim(I) all: 0.121 / Χ2: 1.439 / Net I/av σ(I): 16.673 / Net I/σ(I): 6.7 / Num. measured all: 249206
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.446-2.492.90.44832960.7760.2940.5390.66893
2.49-2.543.20.41934200.830.2640.4970.6996
2.54-2.593.30.41535060.8130.260.4910.73497
2.59-2.643.40.39335260.8680.2440.4640.76398.9
2.64-2.73.40.34635800.8980.2150.4090.77899.4
2.7-2.763.40.31135490.9020.1940.3670.84499.8
2.76-2.833.50.27435940.9260.170.3230.88899.9
2.83-2.93.30.24435710.9310.1560.2911.00299.9
2.9-2.993.50.21535610.9450.1340.2541.09399.9
2.99-3.093.50.18336010.9550.1140.2171.201100
3.09-3.23.70.16435990.9670.0990.1921.327100
3.2-3.323.70.14535660.9730.0870.171.48799.9
3.32-3.483.70.12635830.9770.0760.1481.64499.9
3.48-3.663.60.1135860.9790.0670.1291.90999.7
3.66-3.893.40.09636030.9840.0610.1142.07799.9
3.89-4.193.70.08336190.9870.0510.0982.17699.9
4.19-4.613.80.07335990.9910.0430.0852.34799.9
4.61-5.283.70.06836010.9920.0410.082.19899.9
5.28-6.653.50.06536430.9930.040.0761.96699.8
6.65-503.60.05536930.9950.0320.0652.10199.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHENIXmodel building
HKL-2000data scaling
HKL-2000705bdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XKD

4xkd


Resolution: 2.446→49.636 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 3599 5.05 %
Rwork0.2107 67675 -
obs0.2129 71268 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.46 Å2 / Biso mean: 47.8726 Å2 / Biso min: 17.74 Å2
Refinement stepCycle: final / Resolution: 2.446→49.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11894 0 130 140 12164
Biso mean--79.91 47.54 -
Num. residues----1498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112316
X-RAY DIFFRACTIONf_angle_d1.56716682
X-RAY DIFFRACTIONf_chiral_restr0.0781813
X-RAY DIFFRACTIONf_plane_restr0.0162159
X-RAY DIFFRACTIONf_dihedral_angle_d15.1474486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4461-2.47830.3481120.29212281239386
2.4783-2.51220.35131210.26812491261295
2.5122-2.54810.34241300.26662532266296
2.5481-2.58610.32571410.27732529267098
2.5861-2.62660.35131370.2622594273199
2.6266-2.66960.3281350.25652587272299
2.6696-2.71560.35141380.253126072745100
2.7156-2.7650.3071210.233626712792100
2.765-2.81820.26881550.231325802735100
2.8182-2.87570.28141220.225326212743100
2.8757-2.93820.27871530.229626142767100
2.9382-3.00660.2721490.22326202769100
3.0066-3.08180.26841430.224926182761100
3.0818-3.16510.3171270.220326252752100
3.1651-3.25820.29011550.223626022757100
3.2582-3.36330.25441210.217626402761100
3.3633-3.48350.27131360.217526682804100
3.4835-3.62290.25111300.199826372767100
3.6229-3.78780.261360.191926162752100
3.7878-3.98740.21461450.18426222767100
3.9874-4.23710.2261490.168626312780100
4.2371-4.5640.17781480.157426352783100
4.564-5.02290.18781410.160426582799100
5.0229-5.74880.24811410.194426372778100
5.7488-7.23930.25321460.235726622808100
7.2393-49.64570.24281670.244626912858100

+
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