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- PDB-4xkf: Crystal structure of hemagglutinin from Taiwan (2013) H6N1 influe... -

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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 / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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