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- PDB-4q2z: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE3... -

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Basic information

Entry
Database: PDB / ID: 4q2z
TitleFab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE356, from a non-human primate
Components
  • Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
  • Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
KeywordsIMMUNE SYSTEM / Fab fragment / HIV viral envelope glycoprotein neutralization
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsNavis, M. / Tran, K. / Bale, S. / Phad, G. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. ...Navis, M. / Tran, K. / Bale, S. / Phad, G. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. / Li, Y. / Wyatt, R.T. / Hedestam, G.B.K.
CitationJournal: Plos Pathog. / Year: 2014
Title: HIV-1 Receptor Binding Site-Directed Antibodies Using a VH1-2 Gene Segment Orthologue Are Activated by Env Trimer Immunization.
Authors: Navis, M. / Tran, K. / Bale, S. / Phad, G.E. / Guenaga, J. / Wilson, R. / Soldemo, M. / McKee, K. / Sundling, C. / Mascola, J. / Li, Y. / Wyatt, R.T. / Karlsson Hedestam, G.B.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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: Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
L: Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
A: Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
B: Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody


Theoretical massNumber of molelcules
Total (without water)95,8314
Polymers95,8314
Non-polymers00
Water4,306239
1
H: Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
L: Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody


Theoretical massNumber of molelcules
Total (without water)47,9152
Polymers47,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-25 kcal/mol
Surface area19990 Å2
MethodPISA
2
A: Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody
B: Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody


Theoretical massNumber of molelcules
Total (without water)47,9152
Polymers47,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-25 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.243, 67.909, 69.980
Angle α, β, γ (deg.)92.39, 94.13, 109.69
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Heavy chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody


Mass: 25386.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo Sapiens (human)
#2: Antibody Light chain of Fab fragment of HIV vaccine-elicited CD4bs-directed antibody


Mass: 22528.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo Sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Tri-lithium citrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 18, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→69.62 Å / Num. all: 62555 / Num. obs: 60025 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 33.35 Å2 / Rsym value: 0.045 / Net I/σ(I): 19.2
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.1 / Num. unique all: 2963 / Rsym value: 0.549 / % possible all: 95.8

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KTD

4ktd


Resolution: 1.93→36.991 Å / SU ML: 0.29 / σ(F): 1.98 / Phase error: 32.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 3030 5.05 %RANDOM
Rwork0.2323 ---
obs0.2343 60010 95.94 %-
all-62555 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→36.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 0 239 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056748
X-RAY DIFFRACTIONf_angle_d1.1199190
X-RAY DIFFRACTIONf_dihedral_angle_d15.4132404
X-RAY DIFFRACTIONf_chiral_restr0.0731032
X-RAY DIFFRACTIONf_plane_restr0.0051176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.96020.33161330.3422553X-RAY DIFFRACTION96
1.9602-1.99230.34071390.31962634X-RAY DIFFRACTION96
1.9923-2.02660.32251410.29692602X-RAY DIFFRACTION96
2.0266-2.06350.31981380.30072560X-RAY DIFFRACTION96
2.0635-2.10320.3361390.28992601X-RAY DIFFRACTION96
2.1032-2.14610.33711250.28392624X-RAY DIFFRACTION97
2.1461-2.19280.30611390.28382647X-RAY DIFFRACTION97
2.1928-2.24380.31081180.28042576X-RAY DIFFRACTION96
2.2438-2.29990.29651240.28762642X-RAY DIFFRACTION96
2.2999-2.3620.33641370.27152628X-RAY DIFFRACTION97
2.362-2.43150.33951570.27842625X-RAY DIFFRACTION97
2.4315-2.510.3781370.28112620X-RAY DIFFRACTION97
2.51-2.59970.33611210.27192604X-RAY DIFFRACTION97
2.5997-2.70370.29281410.26962605X-RAY DIFFRACTION96
2.7037-2.82680.30161510.2642616X-RAY DIFFRACTION96
2.8268-2.97570.36091320.26442514X-RAY DIFFRACTION95
2.9757-3.16210.30261430.2652548X-RAY DIFFRACTION94
3.1621-3.40610.30751710.25072494X-RAY DIFFRACTION93
3.4061-3.74850.2491380.21642496X-RAY DIFFRACTION93
3.7485-4.29030.24011320.19012547X-RAY DIFFRACTION94
4.2903-5.40260.19391470.16142611X-RAY DIFFRACTION97
5.4026-36.9980.19171270.18172633X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10160.00810.00420.0561-0.02220.00160.06910.0165-0.01390.0568-0.2111-0.0466-0.06670.1090-0.1426-0.0852-0.22020.1052-0.0031-0.035-3.59456.4064-4.0938
20.05370.01980.01010.0772-0.03850.0218-0.0177-0.1633-0.1279-0.0170.10770.13740.071-0.1773-0-0.18370.0480.03760.09640.05260.11793.0761-5.67557.2132
30.04660.02250.01560.02720.01180.01480.1533-0.2193-0.21990.1298-0.2374-0.3020.0955-0.052300.0790.07240.0519-0.1773-0.1520.020719.4135-31.379913.3678
40.0498-0.04210.01630.02430.0361-0.003-0.039-0.19640.02220.0437-0.0279-0.24070.0161-0.035-00.26420.0118-0.0240.2327-0.00260.055635.1716-32.835822.1709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN H AND RESSEQ 1:213)
2X-RAY DIFFRACTION2(CHAIN L AND RESSEQ 1:208)
3X-RAY DIFFRACTION3(CHAIN A AND RESSEQ 1:213)
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 1:208)

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