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- PDB-5dd1: Crystal structures in an anti-HIV antibody lineage from immunizat... -

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Basic information

Entry
Database: PDB / ID: 5dd1
TitleCrystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques
Components
  • ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN
  • ANTI-HIV ANTIBODY DH570 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HIV HIV-1 gp41 MPER antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsZhang, R. / Verkoczy, L. / Wiehe, K. / Alam, S.M. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C. / Gao, F. / Montefiori, D.C. ...Zhang, R. / Verkoczy, L. / Wiehe, K. / Alam, S.M. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / Parks, R. / Foulger, A. / Tomaras, G. / Keple, T.B. / Moody, M.A. / Liao, H.-X. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI100645-02 United States
CitationJournal: Sci Transl Med / Year: 2016
Title: Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages.
Authors: Zhang, R. / Verkoczy, L. / Wiehe, K. / Munir Alam, S. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C.W. / Zhang, J. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / ...Authors: Zhang, R. / Verkoczy, L. / Wiehe, K. / Munir Alam, S. / Nicely, N.I. / Santra, S. / Bradley, T. / Pemble, C.W. / Zhang, J. / Gao, F. / Montefiori, D.C. / Bouton-Verville, H. / Kelsoe, G. / Larimore, K. / Greenberg, P.D. / Parks, R. / Foulger, A. / Peel, J.N. / Luo, K. / Lu, X. / Trama, A.M. / Vandergrift, N. / Tomaras, G.D. / Kepler, T.B. / Moody, M.A. / Liao, H.X. / Haynes, B.F.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN
L: ANTI-HIV ANTIBODY DH570 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,8592
Polymers47,8592
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.115, 49.168, 54.653
Angle α, β, γ (deg.)90.52, 104.58, 96.57
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody ANTI-HIV ANTIBODY DH570 FAB HEAVY CHAIN


Mass: 24783.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293, Expi293 / Production host: Homo sapiens (human)
#2: Antibody ANTI-HIV ANTIBODY DH570 FAB LIGHT CHAIN


Mass: 23075.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 Expi293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 MES, 14% PEG 4000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 46323 / % possible obs: 81.3 % / Redundancy: 3.7 % / Rsym value: 0.059 / Net I/σ(I): 25.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.6 % / Num. unique all: 2375 / Rsym value: 0.622 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DD0

5dd0


Resolution: 1.597→21.832 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1842 4.3 %
Rwork0.1846 --
obs0.1865 42808 74.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.597→21.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 0 309 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073462
X-RAY DIFFRACTIONf_angle_d1.1394745
X-RAY DIFFRACTIONf_dihedral_angle_d13.5741219
X-RAY DIFFRACTIONf_chiral_restr0.041554
X-RAY DIFFRACTIONf_plane_restr0.005603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5968-1.640.31951200.2632865X-RAY DIFFRACTION68
1.64-1.68820.29511420.24213236X-RAY DIFFRACTION77
1.6882-1.74270.27181530.23163265X-RAY DIFFRACTION78
1.7427-1.8050.25031580.20463466X-RAY DIFFRACTION82
1.805-1.87720.28341500.22513352X-RAY DIFFRACTION79
1.8772-1.96260.306760.2551724X-RAY DIFFRACTION41
1.9626-2.0660.28921530.23253385X-RAY DIFFRACTION81
2.066-2.19530.29641660.22113656X-RAY DIFFRACTION87
2.1953-2.36460.2733910.21182051X-RAY DIFFRACTION49
2.3646-2.60220.23161780.1923922X-RAY DIFFRACTION93
2.6022-2.9780.2361810.19113982X-RAY DIFFRACTION95
2.978-3.74880.2321270.18392792X-RAY DIFFRACTION69
3.7488-21.83380.16051470.13463270X-RAY DIFFRACTION82
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)
13.27790.9567-1.04061.44130.88292.4727-0.41980.67830.86980.09160.31790.324-1.1607-0.58150.02290.9770.0862-0.21950.4920.25140.731431.406112.855749.9098
25.54770.90490.79273.77270.36665.7656-0.33430.37560.3067-0.19190.07240.1427-0.66670.05970.19210.4358-0.0806-0.05520.36480.11390.371137.62274.963153.458
31.673-3.3788-1.37917.95511.71813.7157-0.03420.31740.871-0.01590.6241-0.2413-1.11550.4774-0.39020.7805-0.3663-0.04230.62560.26460.704444.140312.050751.9318
41.2530.33051.71760.62640.80692.8189-0.44140.43740.2789-0.20250.09560.0173-1.20460.63430.26580.4774-0.1206-0.06240.38780.1010.385936.57025.465552.2121
54.8895-0.5259-1.33670.23890.60424.3307-0.10660.1645-0.9148-0.11570.1047-0.14980.9418-0.790.03760.4013-0.1503-0.05530.39320.00030.362610.5545-22.566429.4777
62.83551.3188-0.45783.5072-0.97872.587-0.0151-0.1860.01370.15230.00220.162-0.1845-0.1027-0.00260.24560.02160.01510.2998-0.04190.20413.3718-11.353233.5737
72.65842.3938-0.20712.7327-0.45196.7182-0.35080.45840.0216-0.68540.35530.73330.2644-0.10750.07450.32250.0619-0.00410.226-0.03490.35768.8577-10.837624.8938
83.50532.39340.2382.453-0.50032.3378-0.0638-0.01310.1268-0.04120.01230.0267-0.16090.02490.05230.22320.03860.00890.1996-0.00130.240332.3258-7.973465.3
93.68433.97823.48214.3343.73343.29270.1473-0.18380.27130.1534-0.3250.11920.2012-0.17330.15320.2666-0.05890.02190.37110.01260.262219.3322-21.541555.4192
101.7411-0.1787-1.2430.84930.38165.9127-0.0105-0.1307-0.04030.155-0.0109-0.02080.23770.06720.01320.2032-0.0267-0.0030.198-0.00480.217722.0554-24.733534.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:32 )H1 - 32
2X-RAY DIFFRACTION2( CHAIN H AND RESID 33:52 )H33 - 52
3X-RAY DIFFRACTION3( CHAIN H AND RESID 53:77 )H53 - 77
4X-RAY DIFFRACTION4( CHAIN H AND RESID 78:119 )H78 - 119
5X-RAY DIFFRACTION5( CHAIN H AND RESID 120:134 )H120 - 134
6X-RAY DIFFRACTION6( CHAIN H AND RESID 135:203 )H135 - 203
7X-RAY DIFFRACTION7( CHAIN H AND RESID 204:214 )H204 - 214
8X-RAY DIFFRACTION8( CHAIN L AND RESID 1:101 )L1 - 101
9X-RAY DIFFRACTION9( CHAIN L AND RESID 102:113 )L102 - 113
10X-RAY DIFFRACTION10( CHAIN L AND RESID 114:213 )L114 - 213

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