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- PDB-6uum: Crystal structure of antibody 438-B11 DSS mutant (Cys98A-Cys100aA) -

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Basic information

Entry
Database: PDB / ID: 6uum
TitleCrystal structure of antibody 438-B11 DSS mutant (Cys98A-Cys100aA)
Components
  • B11 DSS Fab Heavy Chain
  • B11 Fab Light Chain
KeywordsIMMUNE SYSTEM / V3 glycan supersite / human antibody / anti-HIV1 neutralizing antibody / VIRAL PROTEIN
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKumar, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2020
Title: A V H 1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite.
Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / ...Authors: Kumar, S. / Ju, B. / Shapero, B. / Lin, X. / Ren, L. / Zhang, L. / Li, D. / Zhou, Z. / Feng, Y. / Sou, C. / Mann, C.J. / Hao, Y. / Sarkar, A. / Hou, J. / Nunnally, C. / Hong, K. / Wang, S. / Ge, X. / Su, B. / Landais, E. / Sok, D. / Zwick, M.B. / He, L. / Zhu, J. / Wilson, I.A. / Shao, Y.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: B11 Fab Light Chain
H: B11 DSS Fab Heavy Chain
A: B11 Fab Light Chain
B: B11 DSS Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,77535
Polymers97,3454
Non-polymers4,43031
Water9,548530
1
F: B11 Fab Light Chain
H: B11 DSS Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,27321
Polymers48,6722
Non-polymers2,60019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-100 kcal/mol
Surface area19810 Å2
MethodPISA
2
A: B11 Fab Light Chain
B: B11 DSS Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,50214
Polymers48,6722
Non-polymers1,83012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-84 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.151, 66.197, 108.856
Angle α, β, γ (deg.)90.000, 117.959, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Antibody , 2 types, 4 molecules FAHB

#1: Antibody B11 Fab Light Chain


Mass: 23444.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody B11 DSS Fab Heavy Chain


Mass: 25227.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 2 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 559 molecules

#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.4 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate (pH=4.16), 0.2M lithium sulfate, 40% %(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76942 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 28.49 Å2 / CC1/2: 0.84 / Rpim(I) all: 0.07 / Rsym value: 0.17 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3836 / CC1/2: 0.46 / Rpim(I) all: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WL2

5wl2


Resolution: 2.1→48.08 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 2008 2.61 %
Rwork0.2293 74904 -
obs0.2303 76912 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 242 530 7498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297097
X-RAY DIFFRACTIONf_angle_d0.59399601
X-RAY DIFFRACTIONf_chiral_restr0.04951064
X-RAY DIFFRACTIONf_plane_restr0.00411205
X-RAY DIFFRACTIONf_dihedral_angle_d16.07832573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.33981450.30365122X-RAY DIFFRACTION96.66
2.15-2.210.28971420.29225363X-RAY DIFFRACTION99.64
2.21-2.270.29231510.29025282X-RAY DIFFRACTION99.67
2.27-2.340.34661370.28095315X-RAY DIFFRACTION99.67
2.34-2.430.31251450.26325349X-RAY DIFFRACTION99.82
2.43-2.530.26271430.24965315X-RAY DIFFRACTION99.78
2.53-2.640.31071410.24975360X-RAY DIFFRACTION99.93
2.64-2.780.28771420.24715346X-RAY DIFFRACTION99.95
2.78-2.950.28851520.25055353X-RAY DIFFRACTION100
2.95-3.180.31330.24245381X-RAY DIFFRACTION99.98
3.18-3.50.25811400.22525388X-RAY DIFFRACTION99.98
3.5-4.010.24251460.20675379X-RAY DIFFRACTION99.98
4.01-5.050.22451450.17115411X-RAY DIFFRACTION100
5.05-48.080.23891460.21245540X-RAY DIFFRACTION99.81

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