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- PDB-5wkz: VH1-69 germline antibody predicted from CR6261 -

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Basic information

Entry
Database: PDB / ID: 5wkz
TitleVH1-69 germline antibody predicted from CR6261
Components
  • Immunoglobulin heavy variable 1-69D,IgG H chain
  • Lambda-chain (AA -20 to 215)
KeywordsIMMUNE SYSTEM / VH1-69 germline / CR6261
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region / 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 C1-set / Immunoglobulin C1-set domain ...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
Immunoglobulin heavy variable 1-69D / Lambda-chain (AA -20 to 215) / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLang, S. / Lee, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI 117675 United States
CitationJournal: To Be Published
Title: Anti-idiotypic antibody K1-18 engages VH1-69 precursor and affinity-matured, anti-stem antibodies through mimicry of the HA stem
Authors: Wilson, I.A. / Lang, S. / Kurosawa, Y. / Ohshima, N. / Ota, T. / Abadejos, J. / Lee, P.S. / Nemazee, D.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Immunoglobulin heavy variable 1-69D,IgG H chain
L: Lambda-chain (AA -20 to 215)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6013
Polymers49,5052
Non-polymers961
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-39 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.233, 84.233, 177.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11H-412-

HOH

21H-527-

HOH

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Components

#1: Antibody Immunoglobulin heavy variable 1-69D,IgG H chain


Mass: 26669.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV1-69D / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0B4J2H0, UniProt: S6BAM6
#2: Antibody Lambda-chain (AA -20 to 215)


Mass: 22835.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A2NUT2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.6M ammonium sulfate 0.08 M sodium acetate pH 4.60 20% glycerol

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 55408 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48.424 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.7
RfactorNum. reflection% reflection
Rfree0.2321 2811 5.08 %
Rwork0.2046 --
obs0.206 55356 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→48.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 5 343 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073296
X-RAY DIFFRACTIONf_angle_d0.9084502
X-RAY DIFFRACTIONf_dihedral_angle_d3.2362302
X-RAY DIFFRACTIONf_chiral_restr0.06517
X-RAY DIFFRACTIONf_plane_restr0.006571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8482-1.88010.36511450.30652464X-RAY DIFFRACTION96
1.8801-1.91430.29951230.27352608X-RAY DIFFRACTION100
1.9143-1.95110.27651490.25562572X-RAY DIFFRACTION100
1.9511-1.99090.29331250.24352603X-RAY DIFFRACTION100
1.9909-2.03420.25271360.24422586X-RAY DIFFRACTION100
2.0342-2.08150.2941520.23112583X-RAY DIFFRACTION100
2.0815-2.13360.28941500.23492598X-RAY DIFFRACTION100
2.1336-2.19130.24461400.22652590X-RAY DIFFRACTION100
2.1913-2.25570.2221470.2192618X-RAY DIFFRACTION100
2.2557-2.32850.23471570.22292578X-RAY DIFFRACTION100
2.3285-2.41180.25151370.2262623X-RAY DIFFRACTION100
2.4118-2.50830.24851330.22652610X-RAY DIFFRACTION100
2.5083-2.62250.2591340.2232642X-RAY DIFFRACTION100
2.6225-2.76070.27081350.22182626X-RAY DIFFRACTION100
2.7607-2.93370.2221480.21762644X-RAY DIFFRACTION100
2.9337-3.16010.21151320.21052643X-RAY DIFFRACTION100
3.1601-3.47810.24811560.19642642X-RAY DIFFRACTION100
3.4781-3.98120.20361340.18552709X-RAY DIFFRACTION100
3.9812-5.0150.18691380.15752730X-RAY DIFFRACTION99
5.015-48.44080.21661400.19862876X-RAY DIFFRACTION99

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