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- PDB-6mts: Crystal structure of VRC43.03 Fab -

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Basic information

Entry
Database: PDB / ID: 6mts
TitleCrystal structure of VRC43.03 Fab
Components
  • Antibody VRC43.03 Fab heavy chain
  • Antibody VRC43.03 Fab light chain
KeywordsIMMUNE SYSTEM / Anti-HIV-1 human antibody / MPER / gp41
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.437 Å
AuthorsKwon, Y.D. / Druz, A. / Law, W.H. / Peng, D. / Doria-Rose, N.A. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody VRC43.03 Fab heavy chain
L: Antibody VRC43.03 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4812
Polymers47,4812
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.424, 69.628, 122.192
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 VRC43.03 Fab heavy chain


Mass: 24576.604 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 VRC43.03 Fab light chain


Mass: 22904.475 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 40% PEG 400, 8% PEG8K, 0.1M HEPES 7.4

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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: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 18236 / % possible obs: 83.2 % / Redundancy: 3.7 % / CC1/2: 0.899 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.086 / Net I/σ(I): 9.3
Reflection shellResolution: 2.41→2.45 Å / Rmerge(I) obs: 0.405 / Num. unique all: 720 / CC1/2: 0.753 / Rpim(I) all: 0.28

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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: 6MTR, VRC43.01

6mtr


Resolution: 2.437→45.923 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.87
RfactorNum. reflection% reflection
Rfree0.2679 1822 10.01 %
Rwork0.242 --
obs0.2447 18197 82.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.437→45.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 34 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023384
X-RAY DIFFRACTIONf_angle_d0.6644629
X-RAY DIFFRACTIONf_dihedral_angle_d7.9271996
X-RAY DIFFRACTIONf_chiral_restr0.044523
X-RAY DIFFRACTIONf_plane_restr0.004586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4369-2.50280.3513980.2886907X-RAY DIFFRACTION61
2.5028-2.57650.3731220.31081095X-RAY DIFFRACTION73
2.5765-2.65960.33811290.29941168X-RAY DIFFRACTION78
2.6596-2.75470.32951370.28511202X-RAY DIFFRACTION80
2.7547-2.86490.34481380.3021241X-RAY DIFFRACTION82
2.8649-2.99530.32761480.27621276X-RAY DIFFRACTION85
2.9953-3.15320.31531400.26651302X-RAY DIFFRACTION86
3.1532-3.35070.25681580.27211371X-RAY DIFFRACTION90
3.3507-3.60930.26591380.2511371X-RAY DIFFRACTION89
3.6093-3.97230.27321520.2241358X-RAY DIFFRACTION89
3.9723-4.54670.23561510.21261351X-RAY DIFFRACTION88
4.5467-5.72660.21011540.21021373X-RAY DIFFRACTION87
5.7266-45.93150.26311570.23461360X-RAY DIFFRACTION83
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)
13.5153-1.1319-1.422.72181.49822.85070.0277-0.24830.03620.06140.0934-0.11420.10640.213-0.04480.3437-0.006-0.05730.55730.05190.4362-20.461511.7196-62.1416
25.0804-1.129-0.51354.5421-2.35338.0689-0.002-0.24870.24210.40170.10330.1053-0.6633-0.4989-0.09920.3970.07090.0490.4637-0.02120.39-21.231512.0537-20.8697
35.415-0.0903-1.59682.65161.10015.9145-0.0333-0.28960.01770.2047-0.0757-0.3728-0.07250.53280.10860.3813-0.0092-0.04980.49220.09560.4662-1.082612.6543-26.5529
47.3474-4.54242.20587.8577-3.51464.3144-0.05010.21480.12050.02140.01980.187-0.24650.16860.03260.2832-0.03390.02270.5059-0.01360.3032-9.290522.2364-54.7151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 130:229 )H130 - 229
2X-RAY DIFFRACTION2( CHAIN H AND RESID 1:114 )H1 - 114
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:108 )L1 - 108
4X-RAY DIFFRACTION4( CHAIN L AND RESID 109:212 )L109 - 212

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