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- PDB-5dd5: Crystal structures in an anti-HIV antibody lineage from immunizat... -

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Basic information

Entry
Database: PDB / ID: 5dd5
TitleCrystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques
Components(ANTI-HIV ANTIBODY DH570.9 FAB HEAVY CHAIN) x 2
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: 1.9 Å
AuthorsNicely, N.I. / Pemble IV, C.W. / 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 DH570.9 FAB HEAVY CHAIN
L: ANTI-HIV ANTIBODY DH570.9 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)48,0422
Polymers48,0422
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-24 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.350, 77.430, 138.420
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 ANTI-HIV ANTIBODY DH570.9 FAB HEAVY CHAIN


Mass: 24829.717 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 DH570.9 FAB HEAVY CHAIN


Mass: 23212.680 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 / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 20% PEG 1500

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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: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→17.7 Å / Num. obs: 33258 / % possible obs: 99.5 % / Redundancy: 8.2 % / Rsym value: 0.219 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DD0

5dd0


Resolution: 1.9→17.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 2000 6.03 %
Rwork0.1981 --
obs0.2018 33163 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→17.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 413 3737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073425
X-RAY DIFFRACTIONf_angle_d1.114671
X-RAY DIFFRACTIONf_dihedral_angle_d13.3181200
X-RAY DIFFRACTIONf_chiral_restr0.041539
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.43011380.3882152X-RAY DIFFRACTION98
1.9475-2.00010.30951400.26482164X-RAY DIFFRACTION99
2.0001-2.05880.27421390.21842179X-RAY DIFFRACTION99
2.0588-2.12520.28141410.22652199X-RAY DIFFRACTION99
2.1252-2.2010.28931410.20942199X-RAY DIFFRACTION99
2.201-2.2890.48571380.32412151X-RAY DIFFRACTION98
2.289-2.39290.2971440.21582232X-RAY DIFFRACTION100
2.3929-2.51870.30681410.21742213X-RAY DIFFRACTION100
2.5187-2.6760.26451430.20712220X-RAY DIFFRACTION100
2.676-2.88180.27981440.19132246X-RAY DIFFRACTION100
2.8818-3.17030.24951440.19422238X-RAY DIFFRACTION100
3.1703-3.62570.23731450.16642268X-RAY DIFFRACTION100
3.6257-4.55510.19691470.1522289X-RAY DIFFRACTION100
4.5551-17.70750.17681550.14732413X-RAY DIFFRACTION100
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)
11.4418-0.49541.05321.8651-0.88893.98220.0276-0.0899-0.0372-0.07220.07730.25910.0054-0.1821-0.12370.117-0.016-0.04210.1280.02080.20974.89247.1135-1.9539
23.1176-0.4893-1.44533.33862.35658.4602-0.0047-0.10680.14540.0840.0454-0.2694-0.3690.3169-0.1980.1343-0.0045-0.05210.11380.03060.19414.83388.91580.2178
30.6852-0.2337-0.05950.1080.1120.7609-0.0686-0.1036-0.00730.04380.064-0.0092-0.12940.00640.04180.1308-0.0121-0.03910.1370.01390.19559.10228.1501-5.9702
41.2649-0.4972-0.13043.7731.582.07050.14020.1491-0.11480.4152-0.54590.45150.3794-0.65730.29090.204-0.11930.04460.3377-0.08740.1988-11.6983-2.4713-32.3131
52.21481.961.54112.8321.74290.9027-0.22210.18750.154-0.84570.21750.0699-0.26590.14650.00760.3195-0.0342-0.05080.18750.01910.158521.5411-10.2529-15.7326
61.20911.23040.68112.67880.73351.8656-0.0196-0.15220.0395-0.0816-0.02130.15430.18860.02810.04730.16160.0205-0.05180.16290.01650.153417.8118-9.7824-7.5795
70.4089-0.28860.82042.1143-0.63121.65320.0022-0.0221-0.10760.13950.0192-0.00950.0568-0.0522-0.00830.1416-0.0214-0.0210.1353-0.00570.10920.9512-4.1486-40.3602
80.6153-0.52830.98792.7656-1.27942.40890.03160.0707-0.07250.0992-0.027-0.2049-0.0130.0790.00640.1036-0.0141-0.00080.1412-0.00360.1632.2103-2.9474-41.4682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:42)
2X-RAY DIFFRACTION2(chain H and resid 43:58)
3X-RAY DIFFRACTION3(chain H and resid 59:125)
4X-RAY DIFFRACTION4(chain H and resid 126:214)
5X-RAY DIFFRACTION5(chain L and resid 1:26)
6X-RAY DIFFRACTION6(chain L and resid 27:106)
7X-RAY DIFFRACTION7(chain L and resid 107:154)
8X-RAY DIFFRACTION8(chain L and resid 155:213)

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