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- PDB-5dd6: Crystal structures in an anti-HIV antibody lineage from immunizat... -

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Basic information

Entry
Database: PDB / ID: 5dd6
TitleCrystal structures in an anti-HIV antibody lineage from immunization of Rhesus macaques
Components
  • ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN
  • ANTI-HIV ANTIBODY DH570.mut58 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 / SYNCHROTRON / Resolution: 1.699 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN
L: ANTI-HIV ANTIBODY DH570.mut58 FAB LIGHT CHAIN
A: ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN
B: ANTI-HIV ANTIBODY DH570.mut58 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)95,6604
Polymers95,6604
Non-polymers00
Water3,819212
1
H: ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN
L: ANTI-HIV ANTIBODY DH570.mut58 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area19540 Å2
MethodPISA
2
A: ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN
B: ANTI-HIV ANTIBODY DH570.mut58 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-25 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.557, 66.128, 73.346
Angle α, β, γ (deg.)116.94, 104.73, 92.90
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody ANTI-HIV ANTIBODY DH570.mut58 FAB HEAVY CHAIN


Mass: 24754.648 Da / Num. of mol.: 2
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.mut58 FAB LIGHT CHAIN


Mass: 23075.584 Da / Num. of mol.: 2
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.: 212 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium/sodium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 87986 / % possible obs: 94.7 % / Redundancy: 2.5 % / Net I/σ(I): 18.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.699→29.391 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 1925 2.19 %
Rwork0.1905 --
obs0.1913 87986 92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→29.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 0 212 6699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076738
X-RAY DIFFRACTIONf_angle_d1.0529206
X-RAY DIFFRACTIONf_dihedral_angle_d12.8912367
X-RAY DIFFRACTIONf_chiral_restr0.0411074
X-RAY DIFFRACTIONf_plane_restr0.0061161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6986-1.74110.28791190.21675487X-RAY DIFFRACTION82
1.7411-1.78810.26031320.21065903X-RAY DIFFRACTION88
1.7881-1.84070.23471470.20616022X-RAY DIFFRACTION91
1.8407-1.90020.25771290.20626167X-RAY DIFFRACTION92
1.9002-1.96810.25321430.21156193X-RAY DIFFRACTION93
1.9681-2.04680.25531400.20726328X-RAY DIFFRACTION94
2.0468-2.140.26111430.20256339X-RAY DIFFRACTION95
2.14-2.25270.24091440.20166344X-RAY DIFFRACTION95
2.2527-2.39380.24161350.20246396X-RAY DIFFRACTION96
2.3938-2.57860.21891480.21056439X-RAY DIFFRACTION96
2.5786-2.83790.26231420.2056468X-RAY DIFFRACTION97
2.8379-3.2480.24291480.20666417X-RAY DIFFRACTION96
3.248-4.09040.18671420.16726389X-RAY DIFFRACTION95
4.0904-29.39510.18421130.15855169X-RAY DIFFRACTION77
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)
13.25362.47083.70311.98592.83024.9363-0.5545-0.9129-0.54731.05980.6458-0.17490.78290.2253-0.11920.77320.4193-0.10870.7573-0.10840.3633-54.7188-81.38341.9066
22.25190.7850.07194.75322.49976.5629-0.31-0.54650.14550.6330.7534-0.67370.37940.5292-0.37750.38470.2202-0.12120.4625-0.22410.3029-52.9071-73.8309-6.5525
32.1092-0.38990.42921.88691.00513.242-0.3932-0.38860.17390.56830.6358-0.750.36440.7826-0.27120.49920.2578-0.15540.613-0.23560.4128-49.6916-73.8088-4.426
4-0.10430.3816-0.43740.1717-0.4714.69550.0873-0.29590.17640.11380.315-0.10331.96990.5544-0.07680.91440.1654-0.18080.4727-0.07190.3396-69.1742-77.486521.1207
53.1416-1.1971-0.42732.83180.73593.1479-0.157-0.22830.32880.34930.3142-0.3540.04570.0846-0.12190.21980.0231-0.03370.1427-0.06060.1886-68.1398-60.3096-6.3873
64.0492-1.25463.49681.4125-0.57856.92920.31160.0964-0.3089-0.11770.00850.04120.48940.1367-0.28070.2480.0035-0.00250.298-0.01620.1574-75.6697-64.264527.2038
73.8099-4.2642-5.14014.88995.89687.11190.1646-0.35660.71860.12830.4532-0.7398-0.17461.392-0.63510.3414-0.09470.02390.4719-0.03740.2733-66.9388-56.975933.9848
82.9785-0.97932.07062.5405-0.65286.07340.1259-0.0286-0.0912-0.01890.0848-0.02980.26170.092-0.20470.194-0.01130.01080.2492-0.00850.1495-74.9114-61.95930.146
93.58340.6386-0.60321.71730.04124.75390.01460.35530.2385-0.10350.04120.0135-0.1336-0.2658-0.04960.1689-0.01-0.00410.1790.02930.1234-41.2341-35.676231.1318
104.5968-2.6839-2.71063.78183.34225.69680.1658-0.05540.06740.087-0.1273-0.16160.16670.1637-0.0420.21370.0066-0.02890.21040.02570.1153-37.1116-39.282536.8143
111.83560.5429-0.670.6926-0.27173.2434-0.0361-0.16450.0059-0.04890.02240.03740.1579-0.02540.06040.1622-0.027-0.01280.13090.01690.1258-38.5328-36.698521.0387
123.42370.07450.70623.3519-0.44594.0219-0.4136-0.01510.5857-0.1780.20150.1266-0.92880.16380.14370.4013-0.0477-0.09140.1935-0.00240.2716-28.0031-23.5161-0.3235
131.6904-0.04340.97231.5992-1.16144.11840.15870.0175-0.0455-0.0621-0.02160.15560.4465-0.5134-0.12950.2119-0.1313-0.01570.3851-0.00160.1783-54.4711-45.167316.0071
147.821-0.21371.02320.87540.29912.8486-0.017-0.03880.1248-0.00390.082-0.0938-0.12950.1377-0.06740.1438-0.0301-0.01590.17420.02220.165-31.2115-35.4712-7.0696
154.4696-1.6039-3.44284.23973.5554.0316-0.1021-0.0485-0.13470.02310.242-0.17080.37850.0927-0.09710.24190.0535-0.03520.22440.020.2688-25.2024-44.0911-5.3
165.17810.1373-0.08040.97430.56762.24620.02920.2722-0.1011-0.13360.05170.0441-0.0350.1439-0.09980.1793-0.0136-0.0180.16470.04290.1922-29.1774-38.3288-9.1099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid 1:27 )A1 - 27
2X-RAY DIFFRACTION2( chain A and resid 28:56 )A28 - 56
3X-RAY DIFFRACTION3( chain A and resid 57:100F )A57 - 213
4X-RAY DIFFRACTION4( chain A and resid 100G:213 )A1 - 213
5X-RAY DIFFRACTION5( chain B and resid 1:105 )B1 - 105
6X-RAY DIFFRACTION6( chain B and resid 106:148 )B106 - 148
7X-RAY DIFFRACTION7( chain B and resid 149:161 )B149 - 161
8X-RAY DIFFRACTION8( chain B and resid 162:213 )B162 - 213
9X-RAY DIFFRACTION9( chain H and resid 1:54 )H1 - 54
10X-RAY DIFFRACTION10( chain H and resid 55:82C )H55 - 214
11X-RAY DIFFRACTION11( chain H and resid 83:133 )H83 - 133
12X-RAY DIFFRACTION12( chain H and resid 134:214 )H134 - 214
13X-RAY DIFFRACTION13( chain L and resid 1:106 )L1 - 106
14X-RAY DIFFRACTION14( chain L and resid 107:147 )L107 - 147
15X-RAY DIFFRACTION15( chain L and resid 148:163 )L148 - 163
16X-RAY DIFFRACTION16( chain L and resid 164:213 )L164 - 213

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