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- PDB-4rfe: Crystal structure of ADCC-potent ANTI-HIV-1 Rhesus macaque antibo... -

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Entry
Database: PDB / ID: 4rfe
TitleCrystal structure of ADCC-potent ANTI-HIV-1 Rhesus macaque antibody JR4 Fab
Components
  • Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
  • Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
KeywordsIMMUNE SYSTEM / HIV-1 GP120 SPECIFIC ANTIBODY / CD4I ANTIBODY / ADCC / HIV-1 ENV / ANTI-HIV-1 ENV ANTIBODY JR4
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWu, X. / Gohain, N. / Tolbert, W.D. / Pazgier, M.
CitationJournal: J.Virol. / Year: 2015
Title: Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.
Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A. ...Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A.L. / Ray, K. / Lewis, G.K. / Pazgier, M.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jun 2, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
H: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
L: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
A: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
B: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
C: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
D: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
E: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
F: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,87120
Polymers190,2688
Non-polymers60312
Water26,2301456
1
H: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
L: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7696
Polymers47,5672
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-53 kcal/mol
Surface area19400 Å2
MethodPISA
2
A: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
B: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6735
Polymers47,5672
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-58 kcal/mol
Surface area19290 Å2
MethodPISA
3
C: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
D: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6023
Polymers47,5672
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-39 kcal/mol
Surface area19190 Å2
MethodPISA
4
E: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
F: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8266
Polymers47,5672
Non-polymers2594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-36 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.418, 79.585, 82.042
Angle α, β, γ (deg.)78.79, 82.89, 65.17
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 8 molecules HACELBDF

#1: Antibody
Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4


Mass: 24847.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey)
Gene: Fab heavy chain of ADCC-potent anti-HIV-1 antibody JR4
Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody
Fab light chain of ADCC-potent anti-HIV-1 antibody JR4


Mass: 22719.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey)
Gene: Fab light chain of ADCC-potent anti-HIV-1 antibody JR4
Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 1468 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1456 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate pH 6.5, 30% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0452 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 28, 2011 / Details: monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0452 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 138309 / Num. obs: 129457 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.35
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.5 / Num. unique all: 7002 / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNN

3tnn


Resolution: 1.91→40.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.97 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 6780 5 %RANDOM
Rwork0.19164 ---
obs0.19442 123383 93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.999 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å21.06 Å2-0.17 Å2
2---0.4 Å20.3 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.91→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12736 0 25 1456 14217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213085
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.95317885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42851687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38924.273454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06151981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5781536
X-RAY DIFFRACTIONr_chiral_restr0.1220.22051
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219764
X-RAY DIFFRACTIONr_mcbond_it1.0071.58459
X-RAY DIFFRACTIONr_mcangle_it1.734213708
X-RAY DIFFRACTIONr_scbond_it2.58734626
X-RAY DIFFRACTIONr_scangle_it3.8824.54177
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 473 -
Rwork0.271 9154 -
obs--95.37 %

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