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- PDB-6u6m: Crystal structure of a vaccine-elicited anti-HIV-1 rhesus macaque... -

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Basic information

Entry
Database: PDB / ID: 6u6m
TitleCrystal structure of a vaccine-elicited anti-HIV-1 rhesus macaque antibody DH840.1
Components
  • DH840.1 Fab heavy chain
  • DH840.1 Fab light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV / ANTIBODY / rhesus macaque / vaccine-elicited
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.683 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
Revision 1.3Nov 6, 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
H: DH840.1 Fab heavy chain
L: DH840.1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,2512
Polymers47,2512
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-25 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 75.080, 93.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody DH840.1 Fab heavy chain


Mass: 24063.883 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 DH840.1 Fab light chain


Mass: 23186.834 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.: 104 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M Sodium chloride, 0.1 M Phosphate/citrate, 20 % w/v PEG 8000

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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 210r / Detector: CCD / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.683→39.57 Å / Num. obs: 12547 / % possible obs: 92.97 % / Redundancy: 4.4 % / Biso Wilson estimate: 35.94 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1794 / Rpim(I) all: 0.08471 / Rrim(I) all: 0.1992 / Net I/σ(I): 12.01
Reflection shellResolution: 2.683→2.779 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6838 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 1171 / CC1/2: 0.795 / Rpim(I) all: 0.3684 / Rrim(I) all: 0.7801 / % possible all: 87.98

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C6X

6c6x


Resolution: 2.683→39.566 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2695 2240 9.96 %
Rwork0.22 --
obs0.2249 12545 89.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.06 Å2 / Biso mean: 36.6525 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 2.683→39.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 0 104 3344
Biso mean---34.22 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023317
X-RAY DIFFRACTIONf_angle_d0.5034529
X-RAY DIFFRACTIONf_chiral_restr0.042526
X-RAY DIFFRACTIONf_plane_restr0.004577
X-RAY DIFFRACTIONf_dihedral_angle_d13.4341990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6832-2.74150.3391270.3047114681
2.7415-2.80530.34381410.2749127493
2.8053-2.87540.30621450.2816132592
2.8754-2.95320.30631420.2626129593
2.9532-3.040.3531410.2608131891
3.04-3.13810.30321440.2443128091
3.1381-3.25020.26021380.2345129991
3.2502-3.38030.28091380.2282127291
3.3803-3.5340.24741450.2177129491
3.534-3.72020.29581370.2159127990
3.7202-3.95310.27011460.2119124990
3.9531-4.2580.28811320.2053126090
4.258-4.68590.21651370.1607126789
4.6859-5.36250.19441450.1939123189
5.3625-6.75080.2561430.2325124388
6.7508-39.560.27051390.1985121787
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)
11.231-0.0227-0.04712.90981.5271.2265-0.1614-0.50840.14130.85070.09310.020.42090.0299-0.17190.4163-0.0507-0.04890.3038-0.06350.279438.25873.45924.233
21.564-1.1103-0.35670.6650.37550.7885-0.0682-0.41680.294-0.27170.1949-0.25010.15360.21610.14910.2227-0.00580.00650.1960.02520.243845.64970.11616.631
30.3041-0.3639-0.09390.40530.49440.28380.1837-0.1249-0.0229-0.0138-0.0835-0.486-0.04460.6070.01810.46620.0153-0.06390.3597-0.00770.36753.72374.85719.753
41.0588-0.9184-0.18641.591-0.18380.7852-0.3025-0.69780.63990.30820.132-0.9661-0.03720.2929-0.11750.31630.0755-0.17340.2981-0.03280.405744.53175.424.2
50.7919-0.2559-0.90122.16551.14811.8796-0.0597-0.251-1.00951.6306-1.320.14050.4532-0.4161-1.54630.03420.37390.051-0.2148-0.09310.149948.01567.27510.261
61.0498-0.7974-0.35541.0670.44440.747-0.20570.08910.09540.58070.0297-0.25340.7146-0.2811-0.02040.2510.00710.00390.3366-0.02460.157334.46675.1919.292
70.01-0.03280.00560.3114-0.12870.0824-0.1676-0.07150.0167-0.5699-0.11990.4395-0.1604-0.19530.00670.4114-0.0382-0.05320.3463-0.01980.2383.14179.49212.674
81.0695-0.4187-0.6650.1592-0.16181.4785-0.025-0.1302-0.05330.280.18140.19190.05770.02980.25810.2278-0.01140.01250.22250.0370.229513.0275.74614.809
90.1207-0.0809-0.31530.36960.32810.51120.2007-1.1046-0.40780.1408-0.0361-0.08010.7533-0.16120.00010.34350.0467-0.00850.54530.09490.27513.16973.37524.084
101.2595-0.94860.82782.24350.91621.82890.04290.4945-0.0094-0.2945-0.0277-0.055-0.2550.15070.00560.22950.02150.00370.26770.05020.249441.32472.622-2.841
111.7785-1.701-0.28281.51470.12340.79480.2880.0991-0.2706-0.3101-0.34090.07430.23280.0516-1.15660.3121-0.0013-0.0610.2495-0.01550.22138.33669.215-3.525
120.94780.1995-0.50790.73970.75090.55540.19790.0236-0.0412-0.2421-0.10770.1466-0.2583-0.18260.00630.1559-0.0103-0.03790.18560.03580.1859.17887.6748.073
131.8355-0.667-0.57420.6472-0.12071.05340.22010.16660.0779-0.2807-0.03820.1251-0.15460.02580.67210.2417-0.021-0.08260.13020.00450.175310.16187.4475.352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:17 )H1 - 17
2X-RAY DIFFRACTION2( CHAIN H AND RESID 18:52 )H18 - 52
3X-RAY DIFFRACTION3( CHAIN H AND RESID 53:72 )H53 - 72
4X-RAY DIFFRACTION4( CHAIN H AND RESID 73:87 )H73 - 87
5X-RAY DIFFRACTION5( CHAIN H AND RESID 88:100 )H88 - 100
6X-RAY DIFFRACTION6( CHAIN H AND RESID 101:119 )H101 - 119
7X-RAY DIFFRACTION7( CHAIN H AND RESID 120:135 )H120 - 135
8X-RAY DIFFRACTION8( CHAIN H AND RESID 136:194 )H136 - 194
9X-RAY DIFFRACTION9( CHAIN H AND RESID 195:212 )H195 - 212
10X-RAY DIFFRACTION10( CHAIN L AND RESID 1:48 )L1 - 48
11X-RAY DIFFRACTION11( CHAIN L AND RESID 49:112 )L49 - 112
12X-RAY DIFFRACTION12( CHAIN L AND RESID 113:154 )L113 - 154
13X-RAY DIFFRACTION13( CHAIN L AND RESID 155:210 )L155 - 210

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