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- PDB-4jo1: Crystal structure of rabbit mAb R56 Fab in complex with V3 crown ... -

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Basic information

Entry
Database: PDB / ID: 4jo1
TitleCrystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 JR-FL gp120
Components
  • gp120
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Ig / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral process / viral envelope
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.033 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2013
Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans.
Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,12611
Polymers94,9256
Non-polymers2005
Water14,502805
1
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5836
Polymers47,4633
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-61 kcal/mol
Surface area19270 Å2
MethodPISA
2
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5435
Polymers47,4633
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-55 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.514, 74.347, 84.438
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'L' and (resseq 2:107 )
211chain 'M' and (resseq 2:107 )
112chain 'L' and (resseq 109:211 ) and (not resseq 159)
212chain 'M' and (resseq 109:211 ) and (not resseq 159)
113chain 'H' and (resseq 2:113 ) and (not resseq 53:54)
213chain 'I' and (resseq 2:113 ) and (not resseq 53:54)
114chain 'H' and (resseq 115:213 ) and (not (resseq 128:135...
214chain 'I' and (resseq 115:213 ) and (not (resseq 128:135...
115chain 'P'
215Chain 'Q'

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain


Mass: 22782.014 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain


Mass: 22173.852 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide gp120


Mass: 2506.816 Da / Num. of mol.: 2
Fragment: third variable region (V3) crown (UNP residues 32-54)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / References: UniProt: Q9YX36
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG6000, 1 M lithium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.033→36.226 Å / Num. all: 56059 / Num. obs: 56014 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.074 / Rsym value: 0.085 / Net I/σ(I): 18.9
Reflection shellResolution: 2.033→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2633 / Rsym value: 0.45 / % possible all: 94.2

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Processing

Software
NameVersionClassification
Blu-Icelikedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X71

2x71


Resolution: 2.033→36.226 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 2834 5.06 %RANDOM
Rwork0.1813 ---
obs0.1834 56014 99.51 %-
all-56059 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.511 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0938 Å2-0 Å2-0.0522 Å2
2---0.5944 Å2-0 Å2
3---0.6882 Å2
Refinement stepCycle: LAST / Resolution: 2.033→36.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 5 805 7252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086598
X-RAY DIFFRACTIONf_angle_d1.1689004
X-RAY DIFFRACTIONf_dihedral_angle_d13.2432276
X-RAY DIFFRACTIONf_chiral_restr0.0811074
X-RAY DIFFRACTIONf_plane_restr0.0051158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L819X-RAY DIFFRACTIONPOSITIONAL
12M819X-RAY DIFFRACTIONPOSITIONAL0.055
21L764X-RAY DIFFRACTIONPOSITIONAL
22M764X-RAY DIFFRACTIONPOSITIONAL0.04
31H825X-RAY DIFFRACTIONPOSITIONAL
32I825X-RAY DIFFRACTIONPOSITIONAL0.04
41H581X-RAY DIFFRACTIONPOSITIONAL
42I581X-RAY DIFFRACTIONPOSITIONAL0.059
51P74X-RAY DIFFRACTIONPOSITIONAL
52Q74X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.033-2.06810.2341390.22262520X-RAY DIFFRACTION95
2.0681-2.10570.32451520.23762631X-RAY DIFFRACTION99
2.1057-2.14620.27891220.22392663X-RAY DIFFRACTION100
2.1462-2.190.24691420.21262645X-RAY DIFFRACTION100
2.19-2.23760.25271330.20542634X-RAY DIFFRACTION100
2.2376-2.28960.2831620.20452655X-RAY DIFFRACTION100
2.2896-2.34690.26511430.20042663X-RAY DIFFRACTION100
2.3469-2.41030.24781490.1942631X-RAY DIFFRACTION100
2.4103-2.48120.21711220.19212653X-RAY DIFFRACTION100
2.4812-2.56130.22961330.19042707X-RAY DIFFRACTION100
2.5613-2.65280.26021540.19442623X-RAY DIFFRACTION100
2.6528-2.7590.27551440.18592664X-RAY DIFFRACTION100
2.759-2.88450.27421420.19032664X-RAY DIFFRACTION100
2.8845-3.03650.21721460.18492676X-RAY DIFFRACTION100
3.0365-3.22660.21921510.17912675X-RAY DIFFRACTION100
3.2266-3.47560.20321410.1762645X-RAY DIFFRACTION100
3.4756-3.8250.20121520.16562689X-RAY DIFFRACTION100
3.825-4.37770.18211270.15892701X-RAY DIFFRACTION100
4.3777-5.51230.17121380.13952714X-RAY DIFFRACTION100
5.5123-36.23210.22051420.19752727X-RAY DIFFRACTION99

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