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- PDB-4qy0: Structure of H10 from human-infecting H10N8 -

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Basic information

Entry
Database: PDB / ID: 4qy0
TitleStructure of H10 from human-infecting H10N8
Components(hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding / membrane 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 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 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,56424
Polymers328,90912
Non-polymers2,65412
Water8,125451
1
A: hemagglutinin
B: hemagglutinin
C: hemagglutinin
D: hemagglutinin
E: hemagglutinin
F: 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 area34730 Å2
ΔGint-129 kcal/mol
Surface area56390 Å2
MethodPISA
2
G: hemagglutinin
H: hemagglutinin
I: hemagglutinin
J: hemagglutinin
K: hemagglutinin
L: 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 area34870 Å2
ΔGint-128 kcal/mol
Surface area56410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.026, 117.991, 123.766
Angle α, β, γ (deg.)98.29, 93.37, 96.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
hemagglutinin


Mass: 34830.293 Da / Num. of mol.: 6
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.: 6
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
#3: 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.: 12
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
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: 2.47→50 Å / Num. all: 137551 / Num. obs: 137551 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.34 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 92.9

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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: 2.47→39.47 Å / FOM work R set: 0.7226 / SU ML: 0.36 / σ(F): 1.96 / Phase error: 33.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 6859 4.99 %RANDOM
Rwork0.2154 ---
all0.2178 137378 --
obs0.2178 137378 93.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.51 Å2 / Biso mean: 48.7 Å2 / Biso min: 13.95 Å2
Refinement stepCycle: LAST / Resolution: 2.47→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23034 0 168 451 23653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523694
X-RAY DIFFRACTIONf_angle_d0.89132016
X-RAY DIFFRACTIONf_chiral_restr0.0633492
X-RAY DIFFRACTIONf_plane_restr0.0034212
X-RAY DIFFRACTIONf_dihedral_angle_d15.9578652
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 (%)
2.4702-2.49830.45831030.42522044214745
2.4983-2.52770.42082290.3884331456092
2.5277-2.55850.43732470.38144370461793
2.5585-2.59090.42312460.35854364461095
2.5909-2.6250.38412450.3564474471995
2.625-2.66090.3582310.34564451468296
2.6609-2.69890.36672670.32584409467696
2.6989-2.73920.3482510.32284525477696
2.7392-2.7820.34972090.29784461467096
2.782-2.82760.34892410.27314510475196
2.8276-2.87630.30282360.25814522475896
2.8763-2.92860.32552320.25774446467896
2.9286-2.98490.2932220.25934450467296
2.9849-3.04580.30642240.25814486471096
3.0458-3.11210.31972310.25834535476696
3.1121-3.18440.34332450.25244430467596
3.1844-3.2640.2952310.23784426465795
3.264-3.35220.29272120.22924454466695
3.3522-3.45080.30792520.22314381463395
3.4508-3.56210.24912290.20474401463094
3.5621-3.68930.24812320.19994424465694
3.6893-3.83690.21622370.18954350458794
3.8369-4.01140.21182260.18394358458494
4.0114-4.22270.22032270.17264373460093
4.2227-4.48690.22862240.16534349457393
4.4869-4.83280.19762180.15844368458694
4.8328-5.31810.20732240.15744444466895
5.3181-6.08520.20632170.17764458467595
6.0852-7.65750.22062560.18224442469896
7.6575-39.47540.19522150.16824483469896
Refinement TLS params.Method: refined / Origin x: -57.5622 Å / Origin y: 21.2423 Å / Origin z: -11.6646 Å
111213212223313233
T0.1215 Å20.0267 Å2-0.0022 Å2-0.1575 Å20.0127 Å2--0.159 Å2
L0.0847 °20.0544 °20.0232 °2-0.1459 °20.0436 °2--0.1381 °2
S-0.0105 Å °0.028 Å °-0.0056 Å °-0.0341 Å °0.0152 Å °-0.0098 Å °-0.0408 Å °0.0106 Å °0 Å °
Refinement TLS groupSelection details: ALL

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