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- PDB-6cez: Crystal Structure of Rabbit Anti-HIV-1 gp120 V2 Fab 16C2 in compl... -

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Basic information

Entry
Database: PDB / ID: 6cez
TitleCrystal Structure of Rabbit Anti-HIV-1 gp120 V2 Fab 16C2 in complex with V2 peptide ConB
Components
  • HIV-1 gp120 V2 Peptide Con B
  • Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2
  • Light chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2
KeywordsIMMUNE SYSTEM / HIV / gp120 / V2 / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.399 Å
AuthorsKong, X. / Pan, R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082676 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI065250 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: PLoS Pathog. / Year: 2018
Title: Select gp120 V2 domain specific antibodies derived from HIV and SIV infection and vaccination inhibit gp120 binding to alpha 4 beta 7.
Authors: Lertjuthaporn, S. / Cicala, C. / Van Ryk, D. / Liu, M. / Yolitz, J. / Wei, D. / Nawaz, F. / Doyle, A. / Horowitch, B. / Park, C. / Lu, S. / Lou, Y. / Wang, S. / Pan, R. / Jiang, X. / ...Authors: Lertjuthaporn, S. / Cicala, C. / Van Ryk, D. / Liu, M. / Yolitz, J. / Wei, D. / Nawaz, F. / Doyle, A. / Horowitch, B. / Park, C. / Lu, S. / Lou, Y. / Wang, S. / Pan, R. / Jiang, X. / Villinger, F. / Byrareddy, S.N. / Santangelo, P.J. / Morris, L. / Wibmer, C.K. / Biris, K. / Mason, R.D. / Gorman, J. / Hiatt, J. / Martinelli, E. / Roederer, M. / Fujikawa, D. / Gorini, G. / Franchini, G. / Arakelyan, A. / Ansari, A.A. / Pattanapanyasat, K. / Kong, X.P. / Fauci, A.S. / Arthos, J.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2
H: Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2
P: HIV-1 gp120 V2 Peptide Con B


Theoretical massNumber of molelcules
Total (without water)47,6083
Polymers47,6083
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-37 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.145, 41.470, 79.893
Angle α, β, γ (deg.)90.00, 91.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2


Mass: 22320.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of rabbit anti-HIV1 gp120 V2 mAb 16C2


Mass: 23367.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 V2 Peptide Con B


Mass: 1920.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23% polyethylene glycol 3350, 0.2 M LiCL, 0.1 M 2-ethanesulfonic acid (MES) pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→39.93 Å / Num. obs: 32149 / % possible obs: 99.8 % / Redundancy: 3.71 % / CC1/2: 0.999 / Rrim(I) all: 0.061 / Net I/av σ(I): 19.07 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 3.73 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 2679 / CC1/2: 0.842 / Rrim(I) all: 0.69 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.399→39.929 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 1638 5.1 %
Rwork0.2372 --
obs0.2402 32149 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→39.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 46 3352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023389
X-RAY DIFFRACTIONf_angle_d0.4254646
X-RAY DIFFRACTIONf_dihedral_angle_d11.6591988
X-RAY DIFFRACTIONf_chiral_restr0.04542
X-RAY DIFFRACTIONf_plane_restr0.005597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3991-2.46970.3541370.3242543X-RAY DIFFRACTION99
2.4697-2.54940.36861280.32432540X-RAY DIFFRACTION100
2.5494-2.64050.36721350.32412528X-RAY DIFFRACTION100
2.6405-2.74620.41531330.31972577X-RAY DIFFRACTION100
2.7462-2.87120.36061350.31522498X-RAY DIFFRACTION100
2.8712-3.02250.37831410.29912565X-RAY DIFFRACTION100
3.0225-3.21180.37011400.29032579X-RAY DIFFRACTION100
3.2118-3.45960.32571330.2692526X-RAY DIFFRACTION100
3.4596-3.80750.34141450.23772527X-RAY DIFFRACTION100
3.8075-4.35790.2111310.20852552X-RAY DIFFRACTION100
4.3579-5.48830.24991380.17862535X-RAY DIFFRACTION100
5.4883-39.93490.2311420.17852541X-RAY DIFFRACTION100

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