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- PDB-6oed: CRYSTAL STRUCTURE OF THE RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB -

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Basic information

Entry
Database: PDB / ID: 6oed
TitleCRYSTAL STRUCTURE OF THE RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB
Components
  • CH55 Fab heavy chain
  • CH55 Fab light chain
KeywordsIMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY CH55 / CD4I ANTIBODY / ADCC / HIV-1 ENV / RV144 VACCINE TRIAL
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.461 Å
AuthorsYan, F. / Van, V. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: Mbio / Year: 2020
Title: Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial.
Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. ...Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. / Lewis, G.K. / Pazgier, M.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CH55 Fab heavy chain
L: CH55 Fab light chain
A: CH55 Fab heavy chain
B: CH55 Fab light chain
C: CH55 Fab heavy chain
D: CH55 Fab light chain


Theoretical massNumber of molelcules
Total (without water)142,3476
Polymers142,3476
Non-polymers00
Water1,51384
1
H: CH55 Fab heavy chain
L: CH55 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4492
Polymers47,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area19450 Å2
MethodPISA
2
A: CH55 Fab heavy chain
B: CH55 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4492
Polymers47,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-24 kcal/mol
Surface area19230 Å2
MethodPISA
3
C: CH55 Fab heavy chain
D: CH55 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4492
Polymers47,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-23 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.990, 74.030, 75.930
Angle α, β, γ (deg.)106.84, 108.43, 91.78
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody CH55 Fab heavy chain


Mass: 24004.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody CH55 Fab light chain


Mass: 23444.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 4000 0.1 M MES pH 5.5 0.15 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 73117 / % possible obs: 76.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.085 / Net I/σ(I): 4.9
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6090 / Rpim(I) all: 0.697 / % possible all: 79.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QEG

3qeg


Resolution: 2.461→42.116 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 35.97
RfactorNum. reflection% reflection
Rfree0.312 3414 4.95 %
Rwork0.2563 --
obs0.2589 68919 65.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.461→42.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 0 84 9840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049993
X-RAY DIFFRACTIONf_angle_d0.90813602
X-RAY DIFFRACTIONf_dihedral_angle_d10.2115970
X-RAY DIFFRACTIONf_chiral_restr0.0491530
X-RAY DIFFRACTIONf_plane_restr0.0061740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.461-2.49620.38631410.36612634X-RAY DIFFRACTION65
2.4962-2.53340.38461460.36462728X-RAY DIFFRACTION64
2.5334-2.5730.39271390.34892691X-RAY DIFFRACTION65
2.573-2.61520.37281490.35062736X-RAY DIFFRACTION67
2.6152-2.66030.35251850.32682708X-RAY DIFFRACTION65
2.6603-2.70870.41041570.3592571X-RAY DIFFRACTION62
2.7087-2.76070.40061280.3522431X-RAY DIFFRACTION60
2.7607-2.81710.38491540.33952194X-RAY DIFFRACTION53
2.8171-2.87830.36671400.32882677X-RAY DIFFRACTION64
2.8783-2.94530.32721300.32212925X-RAY DIFFRACTION70
2.9453-3.01890.38161370.3212896X-RAY DIFFRACTION70
3.0189-3.10050.38621440.31592854X-RAY DIFFRACTION68
3.1005-3.19170.36511630.30362744X-RAY DIFFRACTION66
3.1917-3.29470.35071120.28552671X-RAY DIFFRACTION64
3.2947-3.41240.32391180.26742482X-RAY DIFFRACTION59
3.4124-3.5490.32921540.26382483X-RAY DIFFRACTION60
3.549-3.71040.34431500.2552912X-RAY DIFFRACTION70
3.7104-3.90590.32841190.25162965X-RAY DIFFRACTION70
3.9059-4.15040.29181650.22712816X-RAY DIFFRACTION68
4.1504-4.47050.20671150.1992710X-RAY DIFFRACTION65
4.4705-4.91980.23021210.1962847X-RAY DIFFRACTION67
4.9198-5.63020.27011360.20683086X-RAY DIFFRACTION74
5.6302-7.0880.29571410.24392653X-RAY DIFFRACTION64
7.088-42.12190.28971700.21443091X-RAY DIFFRACTION74
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)
11.15830.73660.04542.253-0.61.1957-0.1792-0.11480.18510.03810.20080.3283-0.1411-0.2464-0.07460.18680.0599-0.01890.3606-0.00820.362329.1086.32819.786
20.62670.2957-0.12332.7757-0.63960.1840.061-0.0872-0.0461-0.03070.01520.1182-0.0057-0.0292-0.07490.3131-0.02960.02090.3087-0.01260.234742.1384-3.626727.9461
31.340.19150.26912.20171.03451.0109-0.1270.1879-0.10260.09110.0959-0.4152-0.17290.22190.04610.3969-0.0506-0.07820.45860.0250.434831.3811-6.4363-18.479
40.53340.15150.11622.11691.010.8691-0.0075-0.0755-0.13930.12830.1552-0.3380.1532-0.0725-0.10030.3119-0.0082-0.02510.32040.03620.352319.3529-17.0784-27.142
51.4963-0.0916-2.09711.8509-0.15991.67550.61940.26920.04980.0598-0.2706-0.1231-0.82320.1143-0.08140.92740.02420.16750.49740.05250.42094.42948.3917-2.2197
61.8311-0.5494-2.01811.23540.292.34840.44270.54730.1256-0.4454-0.2394-0.0467-0.6372-0.64020.06190.68940.14990.00390.50440.04340.3443-11.924145.5656.0033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 214)
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 212)
3X-RAY DIFFRACTION3(chain 'A' and resid 1 through 213)
4X-RAY DIFFRACTION4(chain 'B' and resid 1 through 212)
5X-RAY DIFFRACTION5(chain 'C' and resid 1 through 213)
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 212)

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