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- PDB-6u6o: Crystal structure of a vaccine-elicited anti-HIV-1 rhesus macaque... -

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Entry
Database: PDB / ID: 6u6o
TitleCrystal structure of a vaccine-elicited anti-HIV-1 rhesus macaque antibody DH846
Components
  • DH846 Fab heavy chain
  • DH846 Fab light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV / ANTIBODY / rhesus macaque / vaccine-elicited
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å
AuthorsChen, W.-H. / Choe, M. / Saunders, K.O. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-07-2-0067 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates.
Authors: Cai, F. / Chen, W.H. / Wu, W. / Jones, J.A. / Choe, M. / Gohain, N. / Shen, X. / LaBranche, C. / Eaton, A. / Sutherland, L. / Lee, E.M. / Hernandez, G.E. / Wu, N.R. / Scearce, R. / Seaman, M. ...Authors: Cai, F. / Chen, W.H. / Wu, W. / Jones, J.A. / Choe, M. / Gohain, N. / Shen, X. / LaBranche, C. / Eaton, A. / Sutherland, L. / Lee, E.M. / Hernandez, G.E. / Wu, N.R. / Scearce, R. / Seaman, M.S. / Moody, M.A. / Santra, S. / Wiehe, K. / Tomaras, G.D. / Wagh, K. / Korber, B. / Bonsignori, M. / Montefiori, D.C. / Haynes, B.F. / de Val, N. / Joyce, M.G. / Saunders, K.O.
History
DepositionAug 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: DH846 Fab heavy chain
L: DH846 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4132
Polymers47,4132
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.018, 36.991, 87.921
Angle α, β, γ (deg.)90.000, 111.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody DH846 Fab heavy chain


Mass: 24215.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody DH846 Fab light chain


Mass: 23197.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate, 1.0M Imidazole; MES monohydrate (acid) pH6.5, 25% MPD, 25% PEG 1000, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9288 / % possible obs: 85.2 % / Redundancy: 2.7 % / CC1/2: 0.949 / Net I/σ(I): 5.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1097 / CC1/2: 0.599 / Rpim(I) all: 0.437 / Rrim(I) all: 0.757

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U6M

6u6m


Resolution: 2.806→43.844 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.5
RfactorNum. reflection% reflection
Rfree0.2723 454 5.01 %
Rwork0.2121 --
obs0.2152 9070 84.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.97 Å2 / Biso mean: 50.5319 Å2 / Biso min: 16.13 Å2
Refinement stepCycle: final / Resolution: 2.806→43.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 0 27 3254
Biso mean---30.33 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033308
X-RAY DIFFRACTIONf_angle_d0.6934515
X-RAY DIFFRACTIONf_chiral_restr0.043512
X-RAY DIFFRACTIONf_plane_restr0.004576
X-RAY DIFFRACTIONf_dihedral_angle_d15.051962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.81-3.21160.331440.2626272282
3.2116-4.04580.29991540.2056297488
4.0458-43.840.23631560.1994292084
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)
1-0.0495-0.0699-0.0475-0.19730.09110.06870.04360.0662-0.0921-0.0083-0.1125-0.025-0.19710.000600.2680.0123-0.00180.2658-0.01040.212528.186483.464114.7562
20.0230.0214-0.04740.01290.03990.00740.0117-0.08060.1930.0064-0.05430.0064-0.0004-0.0939-00.30070.0237-0.0060.34380.03270.27029.650272.734934.4956
30.1454-0.11950.16270.225-0.05420.188-0.04920.0463-0.0161-0.02510.00020.1403-0.0247-0.0466-00.2157-0.01090.00910.1802-0.0010.28674.191676.635915.6379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 126)H1 - 126
2X-RAY DIFFRACTION2(chain 'H' and resid 134 through 212)H134 - 212
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 210)L1 - 210

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