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- PDB-4kps: Structure and receptor binding specificity of the hemagglutinin H... -

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Basic information

Entry
Database: PDB / ID: 4kps
TitleStructure and receptor binding specificity of the hemagglutinin H13 from avian influenza A virus H13N6
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding
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
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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsLu, X. / Qi, J. / Shi, Y. / Gao, G.
CitationJournal: J.Virol. / Year: 2013
Title: Structure and Receptor Binding Specificity of Hemagglutinin H13 from Avian Influenza A Virus H13N6
Authors: Lu, X. / Qi, J. / Shi, Y. / Wang, M. / Smith, D.F. / Heimburg-Molinaro, J. / Zhang, Y. / Paulson, J.C. / Xiao, H. / Gao, G.F.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_leaving_atom_flag / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,5229
Polymers165,1556
Non-polymers1,3673
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31690 Å2
ΔGint-156 kcal/mol
Surface area58220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.638, 76.804, 76.380
Angle α, β, γ (deg.)85.60, 82.67, 87.52
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin /


Mass: 36332.820 Da / Num. of mol.: 3 / Fragment: HA1 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Gull/Maryland/704/1977 H13N6 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13103
#2: Protein Hemagglutinin /


Mass: 18718.684 Da / Num. of mol.: 3 / Fragment: HA2 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Gull/Maryland/704/1977 H13N6 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13103

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Sugars , 3 types, 3 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-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/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 1 types, 103 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M L-Proline, 0.1M HEPES, 10% PEG-3350, 0.01M Sodium Bromide, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.587→50 Å / Num. all: 50525 / Num. obs: 50525 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.03 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F23

4f23


Resolution: 2.587→42.455 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7466 / SU ML: 0.36 / σ(F): 0.07 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 2460 5.13 %random
Rwork0.2161 ---
all0.2181 47912 --
obs0.2181 47912 90.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.358 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 296.47 Å2 / Biso mean: 76.847 Å2 / Biso min: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--11.1245 Å2-6.5972 Å2-6.961 Å2
2--24.3599 Å232.3608 Å2
3----13.2354 Å2
Refinement stepCycle: LAST / Resolution: 2.587→42.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11601 0 92 103 11796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511970
X-RAY DIFFRACTIONf_angle_d0.89616215
X-RAY DIFFRACTIONf_chiral_restr0.0971767
X-RAY DIFFRACTIONf_plane_restr0.0022106
X-RAY DIFFRACTIONf_dihedral_angle_d18.7374300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5871-2.63680.36261000.31292150225076
2.6368-2.69060.31981020.28592339244183
2.6906-2.74910.3471310.27892414254586
2.7491-2.81310.36181370.28562461259888
2.8131-2.88340.35291480.27292464261289
2.8834-2.96130.35411410.27022554269591
2.9613-3.04840.31521460.26512565271192
3.0484-3.14680.26121480.23872602275093
3.1468-3.25920.27311680.23472561272994
3.2592-3.38970.26481460.22222643278994
3.3897-3.54390.231340.21412652278695
3.5439-3.73060.23041580.19952633279195
3.7306-3.96420.21681330.18922647278094
3.9642-4.270.20341300.18852603273392
4.27-4.69920.23171240.17372454257888
4.6992-5.37810.21531400.17622577271792
5.3781-6.77130.21531450.20942664280996
6.7713-42.4610.251290.20382469259888
Refinement TLS params.Method: refined / Origin x: 15.1241 Å / Origin y: -26.7787 Å / Origin z: 0.4659 Å
111213212223313233
T0.3549 Å2-0.0301 Å20.0214 Å2-0.2888 Å2-0.0408 Å2--0.3434 Å2
L1.0362 °2-0.3005 °20.4872 °2-0.3127 °2-0.5362 °2--1.1697 °2
S0.0929 Å °0.0229 Å °-0.0126 Å °0.0106 Å °0.0396 Å °0.0489 Å °0.0815 Å °-0.1847 Å °-0.1167 Å °
Refinement TLS groupSelection details: ALL

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