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- PDB-6mtt: Crystal structure of VRC46.01 Fab in complex with gp41 peptide -

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Basic information

Entry
Database: PDB / ID: 6mtt
TitleCrystal structure of VRC46.01 Fab in complex with gp41 peptide
Components
  • Antibody VRC46.01 Fab heavy chain
  • Antibody VRC46.01 Fb light chain
  • RV217 founder virus gp41 peptide
KeywordsIMMUNE SYSTEM / Anti-HIV-1 human antibody / MPER / gp41
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing ...virus-mediated perturbation of host defense response => GO:0019049 / : / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKwon, Y.D. / Druz, A. / Law, W.H. / Peng, D. / 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 1.2Apr 3, 2024Group: 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
L: Antibody VRC46.01 Fb light chain
H: Antibody VRC46.01 Fab heavy chain
P: RV217 founder virus gp41 peptide


Theoretical massNumber of molelcules
Total (without water)51,0013
Polymers51,0013
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-41 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.602, 49.162, 99.967
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-406-

HOH

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Components

#1: Antibody Antibody VRC46.01 Fb light chain


Mass: 23252.709 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 VRC46.01 Fab heavy chain


Mass: 24075.197 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/peptide RV217 founder virus gp41 peptide


Mass: 3673.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: A0A0U3UAX4, UniProt: A7L302*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M potassium iodide

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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: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 62955 / % possible obs: 94.7 % / Redundancy: 3.9 % / CC1/2: 0.757 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.085 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.86 / Num. unique all: 2377 / CC1/2: 0.306 / Rpim(I) all: 0.629

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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: homology model of VRC46.01

Resolution: 1.7→41.257 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.35
RfactorNum. reflection% reflection
Rfree0.2648 1994 3.18 %
Rwork0.2347 --
obs0.2357 62750 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→41.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 273 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043496
X-RAY DIFFRACTIONf_angle_d0.7554768
X-RAY DIFFRACTIONf_dihedral_angle_d9.3592051
X-RAY DIFFRACTIONf_chiral_restr0.049534
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.35751090.3333381X-RAY DIFFRACTION74
1.7425-1.78960.27211290.30753903X-RAY DIFFRACTION86
1.7896-1.84230.30881370.29194163X-RAY DIFFRACTION92
1.8423-1.90180.31411440.27084377X-RAY DIFFRACTION95
1.9018-1.96970.28551460.26384480X-RAY DIFFRACTION97
1.9697-2.04860.28111460.2514448X-RAY DIFFRACTION98
2.0486-2.14180.28331490.24864543X-RAY DIFFRACTION99
2.1418-2.25470.25631490.23874525X-RAY DIFFRACTION99
2.2547-2.3960.28891480.2424527X-RAY DIFFRACTION99
2.396-2.5810.28441520.24614583X-RAY DIFFRACTION99
2.581-2.84060.30951480.24114538X-RAY DIFFRACTION99
2.8406-3.25150.27051490.22844533X-RAY DIFFRACTION98
3.2515-4.0960.21331470.21614477X-RAY DIFFRACTION97
4.096-41.26920.26691410.22754278X-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)
11.27680.33660.68991.77280.98473.9486-0.061-0.1008-0.16110.02540.1248-0.08910.10180.1121-0.06260.472-0.00910.03130.29430.02540.198-9.8424-12.219730.8982
20.85540.1714-0.951.6993-1.25055.9290.0355-0.0320.20570.06260.0540.0339-0.2596-0.372-0.11950.44220.01760.02720.2423-0.01870.2722-7.68627.224619.8988
34.07180.0384-1.2283.7020.12185.08520.14940.45080.0257-0.3269-0.1685-0.18550.2998-0.07080.04030.33730.03850.00220.20890.03240.259-12.0797-20.5083-3.942
45.96873.19751.10375.54270.53621.89350.12340.06150.0177-0.1217-0.14180.22130.0126-0.12770.00850.33480.05280.04080.25330.01640.2263-22.9504-9.944-8.1459
54.86333.6612-2.04997.0385-3.78173.15340.2401-0.27060.05520.1815-0.303-0.0767-0.260.11540.00690.64980.09650.0550.46430.01020.1815-9.1476-4.647344.6376
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 L AND RESID 1:108 )L1 - 108
3X-RAY DIFFRACTION3( CHAIN H AND RESID 125:224 )H125 - 224
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:211 )L109 - 211
5X-RAY DIFFRACTION5( CHAIN P AND RESID 665:683 )P665 - 683

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