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- PDB-4qy1: Structure of H10 from human-infecting H10N8 in complex with avian... -

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Basic information

Entry
Database: PDB / ID: 4qy1
TitleStructure of H10 from human-infecting H10N8 in complex with avian receptor
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding / memebrane fusion
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: 2.594 Å
AuthorsWang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. ...Wang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. / Li, X. / Yan, J. / Shu, Y. / Shi, Y. / Gao, G.F.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for preferential avian receptor binding by the human-infecting H10N8 avian influenza virus
Authors: Wang, M. / Zhang, W. / Qi, J. / Wang, F. / Zhou, J. / Bi, Y. / Wu, Y. / Sun, H. / Liu, J. / Huang, C. / Li, X. / Yan, J. / Shu, Y. / Shi, Y. / Gao, G.F.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_unobs_or_zero_occ_atoms / 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 / _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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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.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
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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
G: hemagglutinin
H: hemagglutinin
I: hemagglutinin
J: hemagglutinin
K: hemagglutinin
L: hemagglutinin
M: hemagglutinin
N: hemagglutinin
O: hemagglutinin
P: hemagglutinin
Q: hemagglutinin
R: hemagglutinin
S: hemagglutinin
T: hemagglutinin
U: hemagglutinin
V: hemagglutinin
W: hemagglutinin
X: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)666,47154
Polymers657,81824
Non-polymers8,65330
Water27,2571513
1
A: hemagglutinin
B: hemagglutinin
C: hemagglutinin
D: hemagglutinin
E: hemagglutinin
F: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,10215
Polymers164,4556
Non-polymers2,6479
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36340 Å2
ΔGint-111 kcal/mol
Surface area57310 Å2
MethodPISA
2
G: hemagglutinin
H: hemagglutinin
I: hemagglutinin
J: hemagglutinin
K: hemagglutinin
L: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,13114
Polymers164,4556
Non-polymers2,6768
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36610 Å2
ΔGint-115 kcal/mol
Surface area57390 Å2
MethodPISA
3
M: hemagglutinin
N: hemagglutinin
O: hemagglutinin
P: hemagglutinin
Q: hemagglutinin
R: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,78212
Polymers164,4556
Non-polymers1,3276
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34700 Å2
ΔGint-131 kcal/mol
Surface area56810 Å2
MethodPISA
4
S: hemagglutinin
T: hemagglutinin
U: hemagglutinin
V: hemagglutinin
W: hemagglutinin
X: hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,45613
Polymers164,4556
Non-polymers2,0027
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35660 Å2
ΔGint-126 kcal/mol
Surface area56980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.257, 111.439, 222.346
Angle α, β, γ (deg.)94.96, 101.17, 91.90
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
hemagglutinin


Mass: 34830.293 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi-Donghu/346/2013(H10N8) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A059T4A1*PLUS
#2: Protein
hemagglutinin


Mass: 19987.896 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi-Donghu/346/2013(H10N8) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A059T4A1*PLUS

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Sugars , 3 types, 30 molecules

#3: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 4
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
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 25
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, 1513 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1513 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15%(w/v) PEG 2000 MME, 0.1M potassium chloride, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.594→50 Å / Num. all: 262929 / Num. obs: 262929 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.4 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BSG

4bsg


Resolution: 2.594→37.073 Å / FOM work R set: 0.7935 / SU ML: 0.35 / σ(F): 1.96 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 13235 5.04 %RANDOM
Rwork0.1972 ---
all0.1996 262752 --
obs0.1996 262752 97.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.54 Å2 / Biso mean: 38.29 Å2 / Biso min: 3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.594→37.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46067 0 558 1513 48138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00547620
X-RAY DIFFRACTIONf_angle_d0.9464370
X-RAY DIFFRACTIONf_chiral_restr0.1217057
X-RAY DIFFRACTIONf_plane_restr0.0048438
X-RAY DIFFRACTIONf_dihedral_angle_d16.81817439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5943-2.62380.39243580.31856589694778
2.6238-2.65470.37024700.38486895698
2.6547-2.6870.3454760.28648243871998
2.687-2.7210.36464920.28848370886298
2.721-2.75680.32044450.27678330877598
2.7568-2.79460.30724650.26598429889498
2.7946-2.83450.33364310.25818369880098
2.8345-2.87680.31844240.25348388881298
2.8768-2.92170.32284680.24468444891298
2.9217-2.96960.3274010.24568332873398
2.9696-3.02080.29454610.24358446890798
3.0208-3.07570.28864590.23368317877698
3.0757-3.13480.2684410.2268367880898
3.1348-3.19880.28584850.21518393887898
3.1988-3.26830.26934390.21438387882698
3.2683-3.34430.26974480.20728448889698
3.3443-3.42780.27374290.21218359878898
3.4278-3.52040.25964490.20228347879698
3.5204-3.6240.22914430.18548429887298
3.624-3.74080.22794360.18278419885598
3.7408-3.87440.2384080.18278435884398
3.8744-4.02930.22714220.18028359878198
4.0293-4.21250.2174470.17288418886598
4.2125-4.43420.20964720.15858336880898
4.4342-4.71150.18344290.15358299872898
4.7115-5.07450.19984370.15378357879497
5.0745-5.58360.21024580.16088262872097
5.5836-6.3880.21923730.1888165853895
6.388-8.03470.21684380.179885518989100
8.0347-37.07690.19444310.178443887498
Refinement TLS params.Method: refined / Origin x: -21.8614 Å / Origin y: 62.2385 Å / Origin z: -17.2672 Å
111213212223313233
T-0.1434 Å20.0034 Å20.0309 Å2-0.1169 Å2-0.0095 Å2--0.0268 Å2
L-0.0699 °2-0.0247 °20.0365 °2-0.0657 °2-0.0067 °2--0.205 °2
S0.0033 Å °0.0202 Å °0.0228 Å °0.0024 Å °0.0188 Å °0.0093 Å °-0.0079 Å °0.0074 Å °0.0378 Å °
Refinement TLS groupSelection details: ALL

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