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- PDB-5f89: Structure of the Unliganded Fab from HIV-1 Neutralising Antibody ... -

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Basic information

Entry
Database: PDB / ID: 5f89
TitleStructure of the Unliganded Fab from HIV-1 Neutralising Antibody CAP248-2B that Binds to the gp120 C-terminus - gp41 Interface
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 / molecular replacement / Resolution: 2.7842 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 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 2.0Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CAP248-2B Heavy Chain
L: CAP248-2B Light Chain
A: CAP248-2B Heavy Chain
B: CAP248-2B Light Chain


Theoretical massNumber of molelcules
Total (without water)96,5334
Polymers96,5334
Non-polymers00
Water41423
1
H: CAP248-2B Heavy Chain
L: CAP248-2B Light Chain


Theoretical massNumber of molelcules
Total (without water)48,2672
Polymers48,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-22 kcal/mol
Surface area20430 Å2
MethodPISA
2
A: CAP248-2B Heavy Chain
B: CAP248-2B Light Chain


Theoretical massNumber of molelcules
Total (without water)48,2672
Polymers48,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-18 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.002, 68.280, 85.731
Angle α, β, γ (deg.)95.59, 99.82, 102.54
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody CAP248-2B Heavy Chain


Mass: 24446.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: B-cell / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody CAP248-2B Light Chain


Mass: 23820.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: B-Cell / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 7.5% PEG4000 12.5% Isopropanol 0.1M Sodium Citrate pH5.6 Cryoprotectant: 30% Ethylene Glycol

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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: 2.78→50 Å / Num. obs: 20522 / % possible obs: 88.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 50.767 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.108 / Rrim(I) all: 0.153 / Χ2: 1.037 / Net I/av σ(I): 6.753 / Net I/σ(I): 6.4 / Num. measured all: 38175
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.78-2.851.60.41.446700.720.40.5650.85857.9
2.85-2.91.70.3417110.7650.3410.4820.89561.9
2.9-2.961.70.3287700.8260.3280.4640.94867.4
2.96-3.021.70.3258220.8370.3250.460.9972
3.02-3.081.70.39550.840.30.4251.01980.1
3.08-3.151.80.3059410.8550.3050.4310.95683.1
3.15-3.231.80.28510170.8240.2850.4031.0789.1
3.23-3.321.90.25810830.8590.2580.3641.07691.8
3.32-3.421.80.21410920.9350.2140.3031.09294.7
3.42-3.531.90.19610880.9270.1960.2771.09496.2
3.53-3.651.90.17411360.9480.1740.2461.05797.1
3.65-3.81.90.15611290.9370.1560.221.07498.7
3.8-3.971.90.13711480.9610.1370.1941.04498.3
3.97-4.181.90.11911160.9560.1190.1691.03298.8
4.18-4.441.90.09911630.970.0990.141.05698.9
4.44-4.791.90.0911490.9710.090.1271.07698.5
4.79-5.271.90.08411320.9720.0840.1181.07799
5.27-6.031.90.07711330.9750.0770.1091.03698.8
6.03-7.591.90.06511390.980.0650.0911.03498.2
7.59-501.90.03611280.9940.0360.0511.00697.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.78 Å41.82 Å
Translation2.78 Å41.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7842→41.822 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 1023 4.99 %
Rwork0.2284 --
obs0.2309 20492 88.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7842→41.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6715 0 0 23 6738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046914
X-RAY DIFFRACTIONf_angle_d0.8129431
X-RAY DIFFRACTIONf_dihedral_angle_d10.5272437
X-RAY DIFFRACTIONf_chiral_restr0.0291081
X-RAY DIFFRACTIONf_plane_restr0.0041196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7842-2.9310.3736940.35311804X-RAY DIFFRACTION57
2.931-3.11460.3981270.3062429X-RAY DIFFRACTION77
3.1146-3.3550.33541510.29132867X-RAY DIFFRACTION91
3.355-3.69240.29361600.26913046X-RAY DIFFRACTION97
3.6924-4.22630.2921650.223134X-RAY DIFFRACTION99
4.2263-5.32290.20961630.17933097X-RAY DIFFRACTION99
5.3229-41.82710.2621630.19373092X-RAY DIFFRACTION98
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)
10.68880.12970.05740.5711-0.21120.8978-0.17140.01510.2085-0.08960.0908-0.0879-0.0452-0.01170.03590.74210.04850.09090.32750.10160.6233-11.506-89.616968.9236
20.56910.37130.05820.418-0.1150.63780.0497-0.0268-0.1618-0.0364-0.10350.07460.43490.11310.01540.82610.08480.13260.31890.05930.7794-24.7629-100.945296.5778
30.82080.5942-0.08540.63950.34710.7125-0.19740.1308-0.1964-0.3242-0.0561-0.15880.26350.0965-0.03810.98340.07870.20780.34470.04540.7926-8.5469-109.084363.6127
40.2845-0.0087-0.06640.40790.53571.1566-0.21280.1454-0.1379-0.1829-0.09540.27990.5083-0.4852-0.10710.92550.08610.13460.24710.11140.6339-34.509-113.438593.3076
50.52970.41640.2330.5604-0.15870.62240.1044-0.0554-0.052-0.3225-0.0672-0.2945-0.164-0.0570.04220.881-0.05560.14150.39140.03630.6798-11.465-83.1585132.1914
60.8440.26510.02650.53440.34560.3461-0.02820.88760.50010.16670.1370.087-0.2622-0.08010.19021.07050.21640.2334-0.1030.22650.874712.6258-78.442899.1862
70.52110.06290.0930.5007-0.21440.78460.09660.0884-0.053-0.2983-0.13270.306-0.1797-0.2420.09560.9660.07150.10940.44490.0450.8271-14.9206-64.4843126.626
80.70950.0389-0.27160.8646-0.23740.3848-0.0318-0.0003-0.08830.07480.05060.1733-0.095-0.10230.07950.88990.08210.11340.240.12750.6958-1.6674-71.485197.9364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 126 )
2X-RAY DIFFRACTION2chain 'H' and (resid 127 through 228 )
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 122 )
4X-RAY DIFFRACTION4chain 'L' and (resid 123 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 228 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 122 )
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 223 )

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