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- PDB-7mf8: Crystal structure of antibody 10E8v4-P100fA Fab in space group P6422 -

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Basic information

Entry
Database: PDB / ID: 7mf8
TitleCrystal structure of antibody 10E8v4-P100fA Fab in space group P6422
Components
  • Antibody 10E8v4 Fab heavy chain
  • Antibody 10E8v4 Fab light chain
KeywordsIMMUNE SYSTEM / Monoclonal antibody 10E8 / MPER / cis-trans isomerization / size-exclusion chromatography
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Antibodies / Year: 2021
Title: Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography.
Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / ...Authors: Do Kwon, Y. / Wang, X.E. / Bender, M.F. / Yang, R. / Li, Y. / McKee, K. / Rawi, R. / O'Dell, S. / Schneck, N.A. / Shaddeau, A. / Zhang, B. / Arnold, F.J. / Connors, M. / Doria-Rose, N.A. / Kwong, P.D. / Lei, Q.P.
History
DepositionApr 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 10E8v4 Fab heavy chain
L: Antibody 10E8v4 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0622
Polymers48,0622
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.690, 95.690, 256.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Antibody Antibody 10E8v4 Fab heavy chain


Mass: 25111.965 Da / Num. of mol.: 1 / Mutation: P100f(kabat numbering)A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-15*05 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Antibody 10E8v4 Fab light chain


Mass: 22950.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGLV3-19*01 / Plasmid: pVRC8400 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 3.6M Sodium formate, 0.1M Sodium acetate 4.6

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36152 / % possible obs: 98.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 52.53 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Χ2: 1.472 / Net I/σ(I): 8 / Num. measured all: 322223
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.248.40.91117790.8870.330.9710.54899.8
2.24-2.289.30.8117790.8920.2760.8570.55399.8
2.28-2.329.60.75617830.8840.2550.7990.56299.9
2.32-2.379.40.63317820.9280.2150.670.58999.9
2.37-2.429.20.57317710.9390.1980.6070.62499.8
2.42-2.489.10.48517790.9390.1670.5140.68599.7
2.48-2.548.80.41318070.9430.1460.4380.75699.9
2.54-2.618.20.32717810.9610.120.3490.9199.6
2.61-2.698.40.27217100.9690.0970.2890.9595.2
2.69-2.779.70.24917980.9780.0830.2631.03599.8
2.77-2.879.70.20318030.9840.0680.2141.20599.9
2.87-2.999.50.16818140.9870.0570.1771.396100
2.99-3.129.30.13818080.9920.0480.1461.69399.9
3.12-3.299.10.11318190.9920.040.121.94199.9
3.29-3.498.80.09418310.9950.0340.12.37499.8
3.49-3.7680.08118280.9950.030.0872.53499.2
3.76-4.148.70.06817540.9960.0240.0732.6694.1
4.14-4.749.10.06118490.9970.0210.0642.8398.7
4.74-5.978.60.05919040.9970.0210.0632.89798.8
5.97-507.40.05719730.9970.0210.0612.99394.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQ9

5iq9


Resolution: 2.2→32.24 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1807 5 %
Rwork0.2072 34313 -
obs0.2087 36120 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.52 Å2 / Biso mean: 65.1339 Å2 / Biso min: 31.09 Å2
Refinement stepCycle: final / Resolution: 2.2→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 0 96 3355
Biso mean---58.43 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.37261360.3122579271599
2.25-2.320.29791370.279526042741100
2.32-2.40.28861380.242426182756100
2.4-2.480.28171360.247325882724100
2.48-2.580.31361390.262326232762100
2.58-2.70.3221320.25812523265597
2.7-2.840.29021390.267326352774100
2.84-3.020.25981390.243826462785100
3.02-3.250.28981400.220226572797100
3.25-3.580.25041400.203626612801100
3.58-4.090.20041360.17832598273496
4.1-5.150.16941440.15592722286699
5.16-32.240.23121510.20922859301097
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)
11.1074-0.0069-0.51971.4062-1.25593.86210.14470.0269-0.1701-0.0444-0.2104-0.05860.11330.20470.04450.4899-0.1216-0.04510.3206-0.00510.385-35.513-10.97218.192
24.22591.08611.36475.35971.57045.51660.359-1.0590.56740.7772-0.53290.6594-0.4673-0.3020.20370.7803-0.28450.09940.6238-0.12730.7143-40.346-17.15655.169
31.80160.76760.59491.3710.63866.66480.25840.00540.0350.1787-0.1399-0.2849-0.07460.2591-0.08990.4816-0.1099-0.03860.30440.00880.4308-19.398-0.05425.125
42.94942.5195-0.08076.3277-1.26743.65490.4902-0.6209-1.15590.7359-0.4934-0.93190.23280.33010.05730.7238-0.2477-0.18610.54670.18370.878-23.579-19.79153.636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:126 )H1 - 126
2X-RAY DIFFRACTION2( CHAIN H AND RESID 138:214 )H138 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 3:113 )L3 - 113
4X-RAY DIFFRACTION4( CHAIN L AND RESID 114:209 )L114 - 209

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