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- PDB-5xhv: Crystal Structure Of Fab S40 In Complex With Influenza Hemaggluti... -

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Basic information

Entry
Database: PDB / ID: 5xhv
TitleCrystal Structure Of Fab S40 In Complex With Influenza Hemagglutinin, HA1 subunit.
Components
  • Hemagglutinin
  • S40 heavy chain
  • S40 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 (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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsLee, C.C. / Wang, A.H.J. / Yu, C.M. / Yang, A.S.
CitationJournal: Sci Rep / Year: 2017
Title: High throughput discovery of influenza virus neutralizing antibodies from phage-displayed synthetic antibody libraries.
Authors: Chen, I.C. / Chiu, Y.K. / Yu, C.M. / Lee, C.C. / Tung, C.P. / Tsou, Y.L. / Huang, Y.J. / Lin, C.L. / Chen, H.S. / Wang, A.H. / Yang, A.S.
History
DepositionApr 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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
E: Hemagglutinin
H: S40 heavy chain
L: S40 light chain
P: S40 heavy chain
Q: S40 light chain


Theoretical massNumber of molelcules
Total (without water)168,1006
Polymers168,1006
Non-polymers00
Water00
1
A: Hemagglutinin
P: S40 heavy chain
Q: S40 light chain


Theoretical massNumber of molelcules
Total (without water)84,0503
Polymers84,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemagglutinin
H: S40 heavy chain
L: S40 light chain


Theoretical massNumber of molelcules
Total (without water)84,0503
Polymers84,0503
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.395, 133.640, 133.136
Angle α, β, γ (deg.)90.00, 110.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin


Mass: 35986.641 Da / Num. of mol.: 2 / Fragment: HA1 subunit (UNP RESIDUES 18-341)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Strain: A/California/07/2009(H1N1) / Gene: HA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: C3W5X2
#2: Antibody S40 heavy chain


Mass: 24445.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
#3: Antibody S40 light chain


Mass: 23618.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human)
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: 4.97 Å3/Da / Density % sol: 75.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8%(w/v) PEG 6000, 1N NaOH, 15% MPD, 0.1 M Na HEPES pH 7.5

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.35→25 Å / Num. obs: 34636 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.3
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W9D, 3HC4, 3GBN

3w9d

3hc4

3gbn


Resolution: 3.35→25 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 26.695 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27452 1826 5 %RANDOM
Rwork0.22987 ---
obs0.23227 34487 76.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 173.528 Å2
Baniso -1Baniso -2Baniso -3
1--5.81 Å2-0 Å2-3.04 Å2
2--22.97 Å2-0 Å2
3----11.64 Å2
Refinement stepCycle: 1 / Resolution: 3.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11100 0 0 0 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911406
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210450
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.94815518
X-RAY DIFFRACTIONr_angle_other_deg0.977324196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.56151434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41424.249466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.072151822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.691542
X-RAY DIFFRACTIONr_chiral_restr0.0790.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.60217.5645754
X-RAY DIFFRACTIONr_mcbond_other11.57717.5645753
X-RAY DIFFRACTIONr_mcangle_it17.94926.3157182
X-RAY DIFFRACTIONr_mcangle_other17.95326.3167183
X-RAY DIFFRACTIONr_scbond_it10.67817.525652
X-RAY DIFFRACTIONr_scbond_other10.67817.525652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.97626.1318337
X-RAY DIFFRACTIONr_long_range_B_refined23.72212271
X-RAY DIFFRACTIONr_long_range_B_other23.72212272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 65 -
Rwork0.258 1283 -
obs--39.29 %

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