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- PDB-7mfb: Crystal structure of antibody 10E8v4 Fab - light chain H31F variant -

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Basic information

Entry
Database: PDB / ID: 7mfb
TitleCrystal structure of antibody 10E8v4 Fab - light chain H31F variant
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: 1.74 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)47,5192
Polymers47,5192
Non-polymers00
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-23 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.800, 56.231, 69.261
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-340-

HOH

21L-423-

HOH

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Components

#1: Antibody Antibody 10E8v4 Fab heavy chain


Mass: 25050.922 Da / Num. of mol.: 1
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: 22467.973 Da / Num. of mol.: 1 / Mutation: H31F
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.: 440 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12% PEG3350, 20% iso-propanol, 0.1M Tris-HCl 8.5

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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: Mar 9, 2020
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
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: 1.74→50 Å / Num. obs: 48111 / % possible obs: 88.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.76 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.118 / Χ2: 0.753 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.783.40.59623940.8260.3160.680.45887.3
1.78-1.813.50.54724600.8680.2880.6220.48592
1.81-1.853.60.45425470.910.2430.5190.54794.5
1.85-1.893.50.4125920.9160.2270.4720.59895.5
1.89-1.933.60.3626310.9240.2010.4150.65996.5
1.93-1.973.70.3126390.9450.1730.3570.68496.8
1.97-2.023.70.2925830.9480.1630.3350.73196.1
2.02-2.073.60.2726070.9510.1560.3140.895.5
2.07-2.143.50.21325330.9680.1260.2490.83393.8
2.14-2.23.20.19224830.9640.1190.2270.94691.3
2.2-2.283.60.17726040.9760.1030.2070.96195.1
2.28-2.383.70.14725460.9820.0850.1710.93994
2.38-2.483.50.12225410.9860.0730.1430.95392.7
2.48-2.613.40.10424760.9880.0640.1230.94191.3
2.61-2.783.10.08823660.9910.0560.1050.92986.8
2.78-2.992.90.07322300.9910.0480.0880.92581.1
2.99-3.292.60.05920030.9910.0410.0730.8573.3
3.29-3.772.70.05319770.9930.0370.0650.78871.9
3.77-4.752.50.04517260.9940.030.0550.58762.3
4.75-5030.04221730.9940.0270.050.39476.7

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Processing

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

5iq9


Resolution: 1.74→40.04 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1968 5 %
Rwork0.2225 --
obs0.2237 39342 71.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 440 3760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123406
X-RAY DIFFRACTIONf_angle_d1.3154646
X-RAY DIFFRACTIONf_dihedral_angle_d6.526475
X-RAY DIFFRACTIONf_chiral_restr0.087514
X-RAY DIFFRACTIONf_plane_restr0.009600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.2947820.31441554X-RAY DIFFRACTION42
1.79-1.840.3109980.27351876X-RAY DIFFRACTION51
1.84-1.890.25391080.24262055X-RAY DIFFRACTION56
1.89-1.950.25891230.23612311X-RAY DIFFRACTION62
1.95-2.020.28831310.21682514X-RAY DIFFRACTION68
2.02-2.10.27891450.2252744X-RAY DIFFRACTION75
2.1-2.20.20961580.23282992X-RAY DIFFRACTION81
2.2-2.310.23961790.22343416X-RAY DIFFRACTION92
2.31-2.460.26481810.21693433X-RAY DIFFRACTION93
2.46-2.650.24171750.2123325X-RAY DIFFRACTION90
2.65-2.920.25651650.21933144X-RAY DIFFRACTION84
2.92-3.340.24761460.21532768X-RAY DIFFRACTION74
3.34-4.20.22041360.21022569X-RAY DIFFRACTION69
4.2-40.040.23731410.22752673X-RAY DIFFRACTION70
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)
12.62341.3883-0.55761.0169-0.80690.09090.1405-0.3870.0570.1673-0.2583-0.0601-0.1150.1670.08140.1937-0.10050.01080.2767-0.05590.1498-40.66751.369728.0111
21.6496-0.05130.64791.5877-0.27023.27180.07580.0699-0.0582-0.29890.02390.07830.3130.2003-0.07030.17710.02390.00190.0531-0.01020.1217-73.1479-16.165922.3454
32.61430.98790.90193.02211.00232.17640.08730.28520.028-0.136-0.1337-0.0994-0.12090.20790.050.09970.00610.01740.2013-0.02040.102-40.0567-1.50397.9095
42.90130.1451-0.88221.3546-0.89483.22870.20260.09380.1430.04240.17920.1219-0.37490.0818-0.14340.2099-0.01260.02480.0154-0.00570.1499-70.5858-3.741912.4992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resi 2:125
2X-RAY DIFFRACTION2chain H and resi 126:250
3X-RAY DIFFRACTION3chain L and resi 2:108
4X-RAY DIFFRACTION4chain L and resi 110:250

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