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- PDB-5xrq: Crystal structure of human monoclonal antibody H3v-47 -

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Basic information

Entry
Database: PDB / ID: 5xrq
TitleCrystal structure of human monoclonal antibody H3v-47
Components
  • Fab H3v-47 heavy chain
  • Fab H3v-47 light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / heavy chain / light chain
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsZhang, H. / Willson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
CitationJournal: Nat Commun / Year: 2018
Title: A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA.
Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, ...Authors: Bangaru, S. / Zhang, H. / Gilchuk, I.M. / Voss, T.G. / Irving, R.P. / Gilchuk, P. / Matta, P. / Zhu, X. / Lang, S. / Nieusma, T. / Richt, J.A. / Albrecht, R.A. / Vanderven, H.A. / Bombardi, R. / Kent, S.J. / Ward, A.B. / Wilson, I.A. / Crowe, J.E.
History
DepositionJun 9, 2017Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 18, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 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
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain
A: Fab H3v-47 heavy chain
B: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)96,9684
Polymers96,9684
Non-polymers00
Water1,910106
1
H: Fab H3v-47 heavy chain
L: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)48,4842
Polymers48,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-23 kcal/mol
Surface area19430 Å2
MethodPISA
2
A: Fab H3v-47 heavy chain
B: Fab H3v-47 light chain


Theoretical massNumber of molelcules
Total (without water)48,4842
Polymers48,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-21 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.126, 135.126, 78.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody Fab H3v-47 heavy chain


Mass: 25227.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody Fab H3v-47 light chain


Mass: 23256.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% (w/v) polyethylene glycol (PEG) 6000, 0.1 M sodium citrate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 50148 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC1/2: 0.891 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Rsym value: 0.11 / Net I/σ(I): 8.1
Reflection shellResolution: 2.57→2.61 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1 / Num. unique obs: 2143 / CC1/2: 0.891 / Rpim(I) all: 0.256 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.6→46.92 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.95
RfactorNum. reflection% reflection
Rfree0.2144 2497 5.14 %
Rwork0.1796 --
obs0.1825 48572 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 0 106 6634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016683
X-RAY DIFFRACTIONf_angle_d1.179100
X-RAY DIFFRACTIONf_dihedral_angle_d15.4534025
X-RAY DIFFRACTIONf_chiral_restr0.0551034
X-RAY DIFFRACTIONf_plane_restr0.0091169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6006-2.65050.30891220.27562248X-RAY DIFFRACTION82
2.6505-2.70450.29291360.28692392X-RAY DIFFRACTION89
2.7045-2.76320.29051210.25592540X-RAY DIFFRACTION93
2.7632-2.82740.27861430.25342534X-RAY DIFFRACTION93
2.8274-2.8980.29891420.25572628X-RAY DIFFRACTION94
2.898-2.97620.25431480.24572553X-RAY DIFFRACTION94
2.9762-3.06350.25781280.21922639X-RAY DIFFRACTION95
3.0635-3.16210.27551570.21692561X-RAY DIFFRACTION94
3.1621-3.27480.25891280.21332604X-RAY DIFFRACTION95
3.2748-3.40550.23771380.19422592X-RAY DIFFRACTION95
3.4055-3.55990.21691420.18582626X-RAY DIFFRACTION95
3.5599-3.74680.21771410.17862565X-RAY DIFFRACTION95
3.7468-3.98030.17631510.16222580X-RAY DIFFRACTION94
3.9803-4.28570.16321360.14742569X-RAY DIFFRACTION95
4.2857-4.71340.15161250.13492624X-RAY DIFFRACTION95
4.7134-5.38710.16091170.13362610X-RAY DIFFRACTION96
5.3871-6.75630.20971500.15372581X-RAY DIFFRACTION94
6.7563-22.43040.22751350.17422603X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -38.4348 Å / Origin y: 66.5561 Å / Origin z: -3.1196 Å
111213212223313233
T0.2719 Å2-0.0573 Å20.0006 Å2-0.3282 Å20.0194 Å2--0.2271 Å2
L0.327 °20.1782 °20.1898 °2-0.1777 °20.1488 °2---0.1187 °2
S-0.0549 Å °0.05 Å °0.0032 Å °-0.0051 Å °0.0459 Å °0.0247 Å °-0.153 Å °0.0379 Å °0.0022 Å °
Refinement TLS groupSelection details: all

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