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- PDB-5dur: Influenza A virus H5 hemagglutinin globular head in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5dur
TitleInfluenza A virus H5 hemagglutinin globular head in complex with antibody 100F4
Components
  • Heavy Chain of Antibody 100F4
  • Hemagglutinin
  • Light Chain of Antibody 100F4
KeywordsIMMUNE SYSTEM / Influenza virus / Antibody / Complex / Neutralize
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
Similarity search - Function
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.82 Å
AuthorsZuo, T. / Sun, J. / Wang, G. / Zhou, P. / Wang, X. / Zhang, L.
CitationJournal: Nat Commun / Year: 2015
Title: Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection
Authors: Zuo, T. / Sun, J. / Wang, G. / Jiang, L. / Zuo, Y. / Li, D. / Shi, X. / Liu, X. / Fan, S. / Ren, H. / Hu, H. / Sun, L. / Zhou, B. / Liang, M. / Zhou, P. / Wang, X. / Zhang, L.
History
DepositionSep 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy Chain of Antibody 100F4
L: Light Chain of Antibody 100F4
C: Hemagglutinin
B: Heavy Chain of Antibody 100F4
D: Light Chain of Antibody 100F4
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1898
Polymers147,7476
Non-polymers4422
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-63 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.094, 101.223, 206.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy Chain of Antibody 100F4


Mass: 24500.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody Light Chain of Antibody 100F4


Mass: 22837.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin


Mass: 26535.771 Da / Num. of mol.: 2 / Fragment: globular head, UNP residues 61-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Anhui/1/2005(H5N1))
Strain: A/Anhui/1/2005(H5N1) / Gene: HA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1WDM0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 4.0M Potassium formate, Tris propane PH 9.0, 2% w/v PEGME 2000

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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 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→40.5 Å / Num. obs: 45011 / % possible obs: 99.8 % / Redundancy: 4.3 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.82→40.5 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2259 5.02 %
Rwork0.2076 --
obs0.2101 45011 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9778 0 28 302 10108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110084
X-RAY DIFFRACTIONf_angle_d1.38513757
X-RAY DIFFRACTIONf_dihedral_angle_d15.1713593
X-RAY DIFFRACTIONf_chiral_restr0.0551554
X-RAY DIFFRACTIONf_plane_restr0.0071759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8176-2.87890.31211240.26882357X-RAY DIFFRACTION89
2.8789-2.94580.28641340.26382688X-RAY DIFFRACTION100
2.9458-3.01950.28471450.26772617X-RAY DIFFRACTION100
3.0195-3.10110.31341330.24992657X-RAY DIFFRACTION100
3.1011-3.19230.30891420.24562688X-RAY DIFFRACTION100
3.1923-3.29530.28741450.22112636X-RAY DIFFRACTION100
3.2953-3.4130.27361420.22322648X-RAY DIFFRACTION100
3.413-3.54960.24741530.20842668X-RAY DIFFRACTION100
3.5496-3.7110.27841520.19842668X-RAY DIFFRACTION100
3.711-3.90660.25571390.19792691X-RAY DIFFRACTION100
3.9066-4.15110.21991380.17592674X-RAY DIFFRACTION100
4.1511-4.47120.20351560.15462695X-RAY DIFFRACTION100
4.4712-4.92050.17421250.152713X-RAY DIFFRACTION100
4.9205-5.63090.20691240.17312736X-RAY DIFFRACTION99
5.6309-7.08810.28091220.2272774X-RAY DIFFRACTION100
7.0881-40.51250.29321850.2462842X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68840.4790.10522.42321.62672.007-0.0145-0.07130.062-0.1071-0.17360.3522-0.0816-0.3474-0.00140.22140.0166-0.02970.28910.0460.312589.9121350.0125646.5712
20.66650.81930.53591.88911.61813.28430.02030.0309-0.11920.20340.06540.07150.3413-0.11640.00490.20590.0203-0.0950.20260.02830.270999.9926335.8433653.6931
33.02621.5485-0.41272.6209-0.2641.9913-0.0749-0.0149-0.2280.01420.0096-0.29860.02660.1644-0.00030.3207-0.033-0.01530.2437-0.06020.230485.0336307.5348626.4528
43.12221.2084-0.18083.3439-0.1532.35980.0192-0.0329-0.3090.01760.0076-0.18750.16070.03620.00040.17420.0085-0.05450.2317-0.03610.1975151.9275377.5066661.1369
52.43950.81751.89911.41710.6272.56940.06890.31550.0996-0.08460.0445-0.0766-0.1490.28660.00420.22690.01660.06960.2342-0.04180.2066121.9683361.4187638.2739
62.25130.35761.12381.05590.41811.6834-0.0697-0.25380.2555-0.0617-0.08130.1558-0.2726-0.2198-0.00030.2490.03510.04650.2239-0.01220.2348107.6981369.8557647.2042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain A
5X-RAY DIFFRACTION5chain B
6X-RAY DIFFRACTION6chain D

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