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- PDB-8d01: The domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13 -

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Basic information

Entry
Database: PDB / ID: 8d01
TitleThe domain-swaped dimer of the HIV-1 CD4bs targeting antibody 21N13
Components
  • 21N13 Fab heavy chain
  • 21N13 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 CD4bs antibody / Domain swap dimer / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsXian, Y. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeINV-008352/OPP1153692 United States
Consortia for HIV/AIDS Vaccine DevelopmentCHAVD 1UM1 AI144462 United States
Other privateP01 AI110657
CitationJournal: To Be Published
Title: Structural and Antigenic Characterization of B Cell Mosaic Env Trimers
Authors: Xian, Y. / Wilson, I.A.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 21N13 Fab heavy chain
L: 21N13 Fab light chain
A: 21N13 Fab heavy chain
B: 21N13 Fab light chain


Theoretical massNumber of molelcules
Total (without water)95,5604
Polymers95,5604
Non-polymers00
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-49 kcal/mol
Surface area37730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)260.367, 45.151, 84.610
Angle α, β, γ (deg.)90.000, 98.609, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Antibody 21N13 Fab heavy chain


Mass: 24366.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody 21N13 Fab light chain


Mass: 23413.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.237M potassium thiocyanate, 10 %(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 34904 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.14 Å2 / Rmerge(I) obs: 0.346 / Rpim(I) all: 0.151 / Rrim(I) all: 0.379 / Χ2: 1.074 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.81.67116980.3490.7521.8361.17599.9
2.54-2.595.51.55117220.430.7171.7121.12299.9
2.59-2.645.91.39217480.5060.6121.5241.157100
2.64-2.695.81.24217150.5210.561.3651.11599.8
2.69-2.755.91.12217380.6970.4971.231.13999.9
2.75-2.826.31.01817420.7330.4311.1071.09799.9
2.82-2.896.30.87316830.8040.370.951.14499.9
2.89-2.966.30.71817440.8530.3040.7811.09799.9
2.96-3.056.30.5817300.9290.2470.6311.077100
3.05-3.156.30.46317410.9370.1980.5051.1100
3.15-3.2660.38217450.9450.1670.4181.121100
3.26-3.395.80.29617250.9580.1310.3251.093100
3.39-3.5560.26117600.9640.1150.2861.12100
3.55-3.736.40.23417390.970.10.2551.016100
3.73-3.976.50.19317280.980.0810.210.94699.9
3.97-4.276.50.15217650.9840.0640.1651.038100
4.27-4.76.20.12317530.9870.0530.1340.95299.9
4.7-5.385.80.12417800.9870.0560.1361.00599.9
5.38-6.786.60.1317840.9860.0550.1421.003100
6.78-5060.12918640.9870.0560.1411.01799.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: F105

Resolution: 2.46→47.68 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2289 1711 4.9 %
Rwork0.1891 33176 -
obs0.1911 34887 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 2.46→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 0 424 6980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226712
X-RAY DIFFRACTIONf_angle_d0.5379135
X-RAY DIFFRACTIONf_chiral_restr0.04261024
X-RAY DIFFRACTIONf_plane_restr0.00441166
X-RAY DIFFRACTIONf_dihedral_angle_d12.50442402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.530.33391100.26821839X-RAY DIFFRACTION65.93
2.53-2.620.31761320.24592819X-RAY DIFFRACTION99.83
2.62-2.710.29091360.2342813X-RAY DIFFRACTION99.7
2.71-2.820.29961460.22952852X-RAY DIFFRACTION99.87
2.82-2.950.30751490.22222781X-RAY DIFFRACTION99.9
2.95-3.10.27371400.22042823X-RAY DIFFRACTION99.97
3.1-3.30.27621520.22342816X-RAY DIFFRACTION100
3.3-3.550.24931400.18222874X-RAY DIFFRACTION100
3.55-3.910.21351460.17272823X-RAY DIFFRACTION100
3.91-4.470.17581570.14322872X-RAY DIFFRACTION99.9
4.47-5.630.15121510.13932893X-RAY DIFFRACTION99.93
5.63-47.680.16281520.17732971X-RAY DIFFRACTION99.78

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