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- PDB-5mp6: Structure of the Unliganded Fab from HIV-1 Neutralizing Antibody ... -

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Basic information

Entry
Database: PDB / ID: 5mp6
TitleStructure of the Unliganded Fab from HIV-1 Neutralizing Antibody CAP248-2B that Binds to the gp120 C-terminus - gp41 Interface, at two Angstrom resolution.
Components
  • CAP248-2B Heavy Chain
  • CAP248-2B Light Chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing antibody / gp120 C-terminus / CAP248 / gp120-gp41 interface
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.959 Å
AuthorsWibmer, C.K. / Gorman, J. / Kwong, P.D.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface Antibody that Caused MPER Exposure through Viral Escape.
Authors: Wibmer, C.K. / Gorman, J. / Ozorowski, G. / Bhiman, J.N. / Sheward, D.J. / Elliott, D.H. / Rouelle, J. / Smira, A. / Joyce, M.G. / Ndabambi, N. / Druz, A. / Asokan, M. / Burton, D.R. / ...Authors: Wibmer, C.K. / Gorman, J. / Ozorowski, G. / Bhiman, J.N. / Sheward, D.J. / Elliott, D.H. / Rouelle, J. / Smira, A. / Joyce, M.G. / Ndabambi, N. / Druz, A. / Asokan, M. / Burton, D.R. / Connors, M. / Abdool Karim, S.S. / Mascola, J.R. / Robinson, J.E. / Ward, A.B. / Williamson, C. / Kwong, P.D. / Morris, L. / Moore, P.L.
History
DepositionDec 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: 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
P: CAP248-2B Heavy Chain
Q: CAP248-2B Light Chain
H: CAP248-2B Heavy Chain
L: CAP248-2B Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,90718
Polymers98,5624
Non-polymers1,34514
Water6,666370
1
P: CAP248-2B Heavy Chain
Q: CAP248-2B Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5695
Polymers49,2812
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-58 kcal/mol
Surface area19580 Å2
MethodPISA
2
H: CAP248-2B Heavy Chain
L: CAP248-2B Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,33813
Polymers49,2812
Non-polymers1,05711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-143 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.003, 85.903, 126.277
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 CAP248-2B Heavy Chain


Mass: 25477.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: B-cell / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody CAP248-2B Light Chain


Mass: 23803.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: B-cell / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: SO4 / Source: (gene. exp.) Homo sapiens (human) / Cell line: B-cell / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 10.25% PEG4000 87.5 mM ammonium sulphate Cryoprotectant: 25% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 57572 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 31.32 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Χ2: 0.965 / Net I/σ(I): 6.7 / Num. measured all: 414268
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.985.70.67928210.7870.30.7440.61399.9
1.98-2.026.30.60828510.8310.2550.660.63199.9
2.02-2.066.70.50828380.8840.2070.5490.69100
2.06-2.17.10.4628420.90.1840.4960.748100
2.1-2.157.30.42628170.9260.1680.4580.762100
2.15-2.27.40.38128870.9340.1490.4090.796100
2.2-2.257.50.34728190.9490.1350.3730.834100
2.25-2.317.50.31528420.9570.1230.3380.864100
2.31-2.387.50.26828850.970.1050.2880.91100
2.38-2.467.50.24728300.9680.0970.2660.975100
2.46-2.547.50.21328850.9770.0830.2291.044100
2.54-2.657.50.18128280.9840.0710.1951.172100
2.65-2.777.40.1528940.9880.0590.1611.047100
2.77-2.917.50.12628800.990.050.1361.167100
2.91-3.17.50.10428820.9930.0410.1121.064100
3.1-3.337.40.0928780.9930.0350.0971.054100
3.33-3.677.40.07629060.9960.030.0821.03100
3.67-4.27.30.06829310.9950.0270.0741.05999.9
4.2-5.297.20.07329580.9910.0290.0781.19599.8
5.29-506.90.08830980.9870.0360.0961.43499.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.6phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QHK and 3B2U

4qhk

3b2u


Resolution: 1.959→41.739 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.02
RfactorNum. reflection% reflection
Rfree0.2399 2000 3.48 %
Rwork0.1978 --
obs0.1992 57501 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.959→41.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 70 370 6995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046824
X-RAY DIFFRACTIONf_angle_d0.7989343
X-RAY DIFFRACTIONf_dihedral_angle_d11.5174044
X-RAY DIFFRACTIONf_chiral_restr0.0491062
X-RAY DIFFRACTIONf_plane_restr0.0051170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9591-2.00810.31641330.25263680X-RAY DIFFRACTION94
2.0081-2.06240.26481400.22773915X-RAY DIFFRACTION100
2.0624-2.12310.2661420.21633930X-RAY DIFFRACTION100
2.1231-2.19160.26571420.21493945X-RAY DIFFRACTION100
2.1916-2.26990.27321430.20733944X-RAY DIFFRACTION100
2.2699-2.36080.24471410.21143943X-RAY DIFFRACTION100
2.3608-2.46820.27851430.20723954X-RAY DIFFRACTION100
2.4682-2.59830.27841420.20573960X-RAY DIFFRACTION100
2.5983-2.76110.26071430.21643965X-RAY DIFFRACTION100
2.7611-2.97420.28961450.22344002X-RAY DIFFRACTION100
2.9742-3.27340.27511430.20813973X-RAY DIFFRACTION100
3.2734-3.74690.21511450.1844032X-RAY DIFFRACTION100
3.7469-4.71960.15831460.16014044X-RAY DIFFRACTION100
4.7196-41.74870.25611520.19814214X-RAY DIFFRACTION99
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)
11.9129-0.18540.05423.2046-2.18411.9760.1241-0.15420.13730.4348-0.084-0.063-0.35340.2395-0.01170.2478-0.0487-0.00250.2243-0.04380.1594100.609795.7148-1.2224
22.489-1.2214-0.41981.66991.09524.0029-0.46410.9008-0.1157-1.29820.3736-0.06910.9737-0.98640.07521.0394-0.3876-0.04340.7070.04420.272393.116667.5662-3.477
34.1659-0.2583-0.80484.5889-1.10844.5267-0.0361-0.15380.16460.10180.17670.0661-0.0533-0.1842-0.11420.1440.02290.00640.2235-0.00070.156279.606698.3081-3.4367
43.4909-0.8861-0.34962.35431.27352.37660.2489-0.4685-0.6129-0.6134-0.1297-0.15690.0135-0.4394-0.09370.9388-0.1574-0.01840.8250.15930.894879.748363.40147.5335
53.2159-1.1847-1.05982.54070.6712.49240.1250.0599-0.149-0.1213-0.05590.09190.1499-0.0491-0.05110.1896-0.0102-0.05760.17560.01390.171379.085882.060130.4685
64.41971.89942.09763.89541.72754.48330.2908-0.80190.06580.4972-0.2818-0.0786-0.0298-0.058-0.00920.2666-0.00420.02810.40340.05580.2313111.066988.007836.1287
74.94470.97310.23233.1658-0.53331.82060.00030.05880.0599-0.19140.04970.05540.0866-0.0378-0.06460.16510.0299-0.00160.14940.0130.131677.8656101.430325.1239
83.7468-2.7680.35865.5155-0.67961.12350.0294-0.233-0.11170.02870.01590.1250.02750.019-0.04180.1463-0.0186-0.02680.2457-0.00730.1642116.913196.256323.6678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 2 through 122 )
2X-RAY DIFFRACTION2chain 'P' and (resid 123 through 224 )
3X-RAY DIFFRACTION3chain 'Q' and (resid 2 through 119 )
4X-RAY DIFFRACTION4chain 'Q' and (resid 120 through 222 )
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 122 )
6X-RAY DIFFRACTION6chain 'H' and (resid 123 through 217 )
7X-RAY DIFFRACTION7chain 'L' and (resid 2 through 119 )
8X-RAY DIFFRACTION8chain 'L' and (resid 120 through 213 )

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