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- PDB-6d2p: Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive don... -

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Basic information

Entry
Database: PDB / ID: 6d2p
TitleCrystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.6 A
Components
  • Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
  • IOMAclass naive CLK31 Fab heavy chain
  • IOMAclass naive CLK31 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 gp120 / engineered outer domain (eOD) / germline targeting / CD4 binding site / IOMA-class naive human germline antibody / viral-protein complex / healthy HIV-1 negative donor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSarkar, A. / Wilson, I.A.
CitationJournal: Sci Transl Med / Year: 2018
Title: The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen.
Authors: Havenar-Daughton, C. / Sarkar, A. / Kulp, D.W. / Toy, L. / Hu, X. / Deresa, I. / Kalyuzhniy, O. / Kaushik, K. / Upadhyay, A.A. / Menis, S. / Landais, E. / Cao, L. / Diedrich, J.K. / Kumar, S. ...Authors: Havenar-Daughton, C. / Sarkar, A. / Kulp, D.W. / Toy, L. / Hu, X. / Deresa, I. / Kalyuzhniy, O. / Kaushik, K. / Upadhyay, A.A. / Menis, S. / Landais, E. / Cao, L. / Diedrich, J.K. / Kumar, S. / Schiffner, T. / Reiss, S.M. / Seumois, G. / Yates, J.R. / Paulson, J.C. / Bosinger, S.E. / Wilson, I.A. / Schief, W.R. / Crotty, S.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
H: IOMAclass naive CLK31 Fab heavy chain
L: IOMAclass naive CLK31 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4658
Polymers66,0053
Non-polymers4605
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-23 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.300, 66.636, 76.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8


Mass: 19889.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)
#2: Antibody IOMAclass naive CLK31 Fab heavy chain


Mass: 23697.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#3: Antibody IOMAclass naive CLK31 Fab light chain


Mass: 22417.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: pH 5.0 of 20% w/v PEG6000, 0.1M citric acid (pH 4.0)

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→38.26 Å / Num. obs: 21985 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.92 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 10.8 % / Num. unique obs: 2165 / CC1/2: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000705bdata reduction
HKL-2000705bdata scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IES

5ies


Resolution: 2.6→38.259 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 1087 5 %
Rwork0.2133 --
obs0.216 21741 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 30 113 4568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034571
X-RAY DIFFRACTIONf_angle_d0.6186209
X-RAY DIFFRACTIONf_dihedral_angle_d11.3551607
X-RAY DIFFRACTIONf_chiral_restr0.024697
X-RAY DIFFRACTIONf_plane_restr0.004794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.32081320.27532504X-RAY DIFFRACTION99
2.7183-2.86160.34631330.27612534X-RAY DIFFRACTION100
2.8616-3.04080.33011350.26932559X-RAY DIFFRACTION100
3.0408-3.27550.3291340.25522546X-RAY DIFFRACTION100
3.2755-3.60490.28821350.22612562X-RAY DIFFRACTION100
3.6049-4.1260.26981360.19562584X-RAY DIFFRACTION100
4.126-5.19620.21731380.16212623X-RAY DIFFRACTION100
5.1962-38.26310.19371440.1882742X-RAY DIFFRACTION100

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