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- PDB-6mtq: Crystal structure of VRC42.N1 Fab in complex with T117-F MPER scaffold -

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Basic information

Entry
Database: PDB / ID: 6mtq
TitleCrystal structure of VRC42.N1 Fab in complex with T117-F MPER scaffold
Components
  • Antibody VRC42.N1 Fab heavy chain
  • Antibody VRC42.N1 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: 2.7 Å
AuthorsKwon, Y.D. / Law, W.H. / Veradi, R. / 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.N1 Fab light chain
H: Antibody VRC42.N1 Fab heavy chain
T: VRC42 epitope T117-F scaffold


Theoretical massNumber of molelcules
Total (without water)65,8433
Polymers65,8433
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-31 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.206, 70.257, 212.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Antibody VRC42.N1 Fab light chain


Mass: 23507.051 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.N1 Fab heavy chain


Mass: 24117.211 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.: 59 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 400, 0.1M Magnesium sulfate, 2M Ammonium sulfate, 0.1M Tris, pH 8.5

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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: Nov 17, 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: 2.7→50 Å / Num. obs: 18549 / % possible obs: 97.3 % / Redundancy: 2.9 % / CC1/2: 0.864 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.099 / Net I/σ(I): 9.3
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.717 / CC1/2: 0.521 / Rpim(I) all: 0.499

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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: 2.7→36.847 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.14
RfactorNum. reflection% reflection
Rfree0.2593 919 5 %
Rwork0.2062 --
obs0.2088 18386 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→36.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 0 59 4602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024775
X-RAY DIFFRACTIONf_angle_d0.4926531
X-RAY DIFFRACTIONf_dihedral_angle_d14.4332878
X-RAY DIFFRACTIONf_chiral_restr0.044733
X-RAY DIFFRACTIONf_plane_restr0.004846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.84240.3461260.29642414X-RAY DIFFRACTION96
2.8424-3.02040.30031290.27332450X-RAY DIFFRACTION97
3.0204-3.25340.30121310.23922476X-RAY DIFFRACTION98
3.2534-3.58060.27531320.22362504X-RAY DIFFRACTION98
3.5806-4.09810.25971310.1962499X-RAY DIFFRACTION98
4.0981-5.1610.24171330.1642524X-RAY DIFFRACTION97
5.161-36.85050.21851370.19152600X-RAY DIFFRACTION95
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)
12.07080.76791.38573.61131.46995.49040.06490.0214-0.1002-0.16230.0152-0.1599-0.06610.3722-0.08280.16140.00810.03330.23270.06250.288425.57682.6159-44.5197
21.55060.5971-0.57456.2726-4.79994.342-0.154-0.179-0.10510.0871-0.1376-0.4113-0.09550.16590.34880.2579-0.0136-0.03080.4210.00730.299134.326-4.3416-11.4069
30.17110.0584-0.0022.0223-1.50165.79580.0752-0.1516-0.0887-0.0023-0.06150.3590.3582-0.3866-0.04520.2269-0.0913-0.00330.3762-0.04870.38247.9567-7.7235-36.0618
46.04784.15533.05216.14793.14485.91640.1077-0.05760.24440.22950.01740.1154-0.4006-0.024-0.0990.32670.02610.04620.37320.08180.302220.71270.5813-3.431
53.8575-0.4777-1.36214.40371.27824.8613-0.04860.28410.0932-0.4665-0.00050.2069-0.2707-0.04810.03470.46460.0489-0.07540.3493-0.00870.336613.70012.8428-71.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:114 )H1 - 114
2X-RAY DIFFRACTION2( CHAIN H AND RESID 125:227 )H125 - 227
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:108 )L1 - 108
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:211 )L109 - 211
5X-RAY DIFFRACTION5( CHAIN T AND RESID 11:166 )T11 - 166

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