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- PDB-6mto: Crystal structure of VRC42.01 Fab in complex with T117-F MPER scaffold -

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Basic information

Entry
Database: PDB / ID: 6mto
TitleCrystal structure of VRC42.01 Fab in complex with T117-F MPER scaffold
Components
  • Antibody VRC42.01 Fab heavy chain
  • Antibody VRC42.01 Fab light chain
  • VRC42 epitope T117-F scaffold
KeywordsIMMUNE SYSTEM / Anti-HIV-1 human antibody / MPER / gp41
Function / homologyMannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.634 Å
AuthorsKwon, Y.D. / Druz, A. / Law, W.H. / Peng, D. / Zhang, B. / Doria-Rose, N.A. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: Immunity / Year: 2019
Title: Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual.
Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. ...Authors: Krebs, S.J. / Kwon, Y.D. / Schramm, C.A. / Law, W.H. / Donofrio, G. / Zhou, K.H. / Gift, S. / Dussupt, V. / Georgiev, I.S. / Schatzle, S. / McDaniel, J.R. / Lai, Y.T. / Sastry, M. / Zhang, B. / Jarosinski, M.C. / Ransier, A. / Chenine, A.L. / Asokan, M. / Bailer, R.T. / Bose, M. / Cagigi, A. / Cale, E.M. / Chuang, G.Y. / Darko, S. / Driscoll, J.I. / Druz, A. / Gorman, J. / Laboune, F. / Louder, M.K. / McKee, K. / Mendez, L. / Moody, M.A. / O'Sullivan, A.M. / Owen, C. / Peng, D. / Rawi, R. / Sanders-Buell, E. / Shen, C.H. / Shiakolas, A.R. / Stephens, T. / Tsybovsky, Y. / Tucker, C. / Verardi, R. / Wang, K. / Zhou, J. / Zhou, T. / Georgiou, G. / Alam, S.M. / Haynes, B.F. / Rolland, M. / Matyas, G.R. / Polonis, V.R. / McDermott, A.B. / Douek, D.C. / Shapiro, L. / Tovanabutra, S. / Michael, N.L. / Mascola, J.R. / Robb, M.L. / Kwong, P.D. / Doria-Rose, N.A.
History
DepositionOct 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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
Revision 1.3Oct 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
L: Antibody VRC42.01 Fab light chain
H: Antibody VRC42.01 Fab heavy chain
T: VRC42 epitope T117-F scaffold


Theoretical massNumber of molelcules
Total (without water)65,4193
Polymers65,4193
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-40 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.280, 47.418, 79.791
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Antibody VRC42.01 Fab light chain


Mass: 23482.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Antibody VRC42.01 Fab heavy chain


Mass: 23717.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein VRC42 epitope T117-F scaffold


Mass: 18218.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 10% PEG 400, 2% PEG 3350, 0.1M Na Acetate 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2017
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: 2.63→50 Å / Num. obs: 17700 / % possible obs: 92.4 % / Redundancy: 3.4 % / CC1/2: 0.867 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Net I/σ(I): 11.3
Reflection shellResolution: 2.63→2.7 Å / Rmerge(I) obs: 0.556 / Num. unique all: 580 / CC1/2: 0.555 / Rpim(I) all: 0.479

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MTP, VRC42.04

6mtp


Resolution: 2.634→30.263 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.55
RfactorNum. reflection% reflection
Rfree0.2694 1785 10.09 %
Rwork0.2209 --
obs0.2257 17691 91.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.634→30.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 0 9 4541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024649
X-RAY DIFFRACTIONf_angle_d0.5286330
X-RAY DIFFRACTIONf_dihedral_angle_d13.3832771
X-RAY DIFFRACTIONf_chiral_restr0.042701
X-RAY DIFFRACTIONf_plane_restr0.005821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6336-2.70480.3781770.3461694X-RAY DIFFRACTION53
2.7048-2.78430.36071140.33371044X-RAY DIFFRACTION78
2.7843-2.87410.40331320.34321159X-RAY DIFFRACTION89
2.8741-2.97680.34521500.29691278X-RAY DIFFRACTION95
2.9768-3.09590.35951440.30941296X-RAY DIFFRACTION98
3.0959-3.23660.34821360.29051307X-RAY DIFFRACTION98
3.2366-3.4070.31231550.2691321X-RAY DIFFRACTION98
3.407-3.62020.27931460.24561302X-RAY DIFFRACTION98
3.6202-3.89910.24581460.22871308X-RAY DIFFRACTION98
3.8991-4.29050.25241430.19741323X-RAY DIFFRACTION98
4.2905-4.90910.24411490.17371292X-RAY DIFFRACTION97
4.9091-6.17630.2691510.19951318X-RAY DIFFRACTION96
6.1763-30.26450.22541420.19381264X-RAY DIFFRACTION90
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)
14.9966-4.43382.92153.8736-1.00213.72980.03730.1684-0.7735-0.2820.16910.65610.31050.0317-0.2720.54-0.1091-0.00330.4665-0.12120.9766183.3627-33.187677.0447
25.57380.58052.51482.35370.21517.0551-0.3299-0.041.12640.34850.06050.4169-0.82810.1340.48310.64430.02760.00280.3978-0.06271.0206183.1002-12.575483.892
35.34290.02792.18734.01391.65756.41840.2299-0.6129-0.73271.4638-0.298-0.49510.6422-0.18120.17290.9829-0.0925-0.05530.41960.02040.6986203.4793-34.8279105.6327
48.4234-0.61130.78056.5511.07682.46760.2557-0.10780.15751.0493-0.1648-0.99440.14050.4716-0.17490.8903-0.1262-0.23120.5888-0.00930.8955212.5962-21.6188101.7726
58.3697-0.8036-1.32533.7965-0.12086.9773-0.21141.1265-0.6338-0.3895-0.33360.89770.5524-1.28010.49240.7059-0.1296-0.22481.0351-0.18211.1906162.8081-28.264356.979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:119 )H1 - 119
2X-RAY DIFFRACTION2( CHAIN L AND RESID 1:107 )L1 - 107
3X-RAY DIFFRACTION3( CHAIN H AND RESID 120:217 )H120 - 217
4X-RAY DIFFRACTION4( CHAIN L AND RESID 108:211 )L108 - 211
5X-RAY DIFFRACTION5( CHAIN T AND RESID 11:167 )T11 - 167

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