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- PDB-6fy2: Crystal structure of a V2p-reactive RV144 vaccine-like antibody, ... -

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Basic information

Entry
Database: PDB / ID: 6fy2
TitleCrystal structure of a V2p-reactive RV144 vaccine-like antibody, CAP228-16H, in complex with a heterologous CAP225 V1V2
Components
  • CAP225 Scaffolded V1V2
  • CAP228-16H Heavy Chain
  • CAP228-16H Light Chain
KeywordsIMMUNE SYSTEM / Fab / HIV-1 Envelope V1V2
Function / homologyIgG-binding B / B domain / cell wall / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CAP225 Scaffolded V1V2
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsWibmer, C.K. / Moore, P.L. / Morris, L.
Funding support United States, South Africa, 3items
OrganizationGrant numberCountry
National Institutes of HealthAI104387-01 United States
Poliomyelitis Research Foundation15/83 South Africa
NHLS Research Trust South Africa
CitationJournal: Nat Commun / Year: 2018
Title: Common helical V1V2 conformations of HIV-1 Envelope expose the alpha 4 beta 7 binding site on intact virions.
Authors: Wibmer, C.K. / Richardson, S.I. / Yolitz, J. / Cicala, C. / Arthos, J. / Moore, P.L. / Morris, L.
History
DepositionMar 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 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
H: CAP228-16H Heavy Chain
L: CAP228-16H Light Chain
P: CAP225 Scaffolded V1V2
X: CAP228-16H Heavy Chain
Y: CAP228-16H Light Chain
Z: CAP225 Scaffolded V1V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,90313
Polymers126,2466
Non-polymers6577
Water7,314406
1
H: CAP228-16H Heavy Chain
L: CAP228-16H Light Chain
P: CAP225 Scaffolded V1V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5928
Polymers63,1233
Non-polymers4685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-52 kcal/mol
Surface area20360 Å2
MethodPISA
2
X: CAP228-16H Heavy Chain
Y: CAP228-16H Light Chain
Z: CAP225 Scaffolded V1V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3115
Polymers63,1233
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-42 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.354, 41.757, 144.524
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules PZ

#3: Protein CAP225 Scaffolded V1V2


Mass: 15330.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: CAP225 / Gene: Env / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnTI- / References: UniProt: A0A3F2YM25*PLUS

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Antibody , 2 types, 4 molecules HXLY

#1: Antibody CAP228-16H Heavy Chain


Mass: 25145.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGHV5-51 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#2: Antibody CAP228-16H Light Chain


Mass: 22647.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Donor CAP228 / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B cell / Gene: IGLV3-21 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 413 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.62 Å3/Da / Density % sol: 53.04 % / Description: Beautiful
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES NaOH (pH7.5), 20% PEG8000, 0.2 M ammonium sulphate, 10% isopropanol, and cryoprotected with 20% glycerol

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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: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58982 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.952 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.121 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.206 / Mean I/σ(I) obs: 4 / CC1/2: 0.56 / Rpim(I) all: 0.743 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13.2998refinement
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200009079

Resolution: 2.301→36.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.66
RfactorNum. reflection% reflection
Rfree0.2165 1919 3.41 %
Rwork0.1896 --
obs0.1905 56300 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.301→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6792 0 39 406 7237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026998
X-RAY DIFFRACTIONf_angle_d0.6159542
X-RAY DIFFRACTIONf_dihedral_angle_d14.3154166
X-RAY DIFFRACTIONf_chiral_restr0.0481074
X-RAY DIFFRACTIONf_plane_restr0.0041212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3014-2.35890.2541220.25413371X-RAY DIFFRACTION85
2.3589-2.42270.27111260.24963580X-RAY DIFFRACTION89
2.4227-2.4940.3171250.24633655X-RAY DIFFRACTION90
2.494-2.57440.26931310.23993702X-RAY DIFFRACTION92
2.5744-2.66640.27451310.23213726X-RAY DIFFRACTION93
2.6664-2.77320.24281370.2233905X-RAY DIFFRACTION95
2.7732-2.89930.26951400.21173881X-RAY DIFFRACTION97
2.8993-3.05210.26221380.19613918X-RAY DIFFRACTION97
3.0521-3.24320.22581430.19884033X-RAY DIFFRACTION98
3.2432-3.49340.19331440.17424060X-RAY DIFFRACTION99
3.4934-3.84460.18871410.16324062X-RAY DIFFRACTION100
3.8446-4.40010.18031440.15084086X-RAY DIFFRACTION100
4.4001-5.54050.1641460.14534131X-RAY DIFFRACTION99
5.5405-36.09470.22171510.21724271X-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)
14.5389-0.5007-0.20931.3642-0.04492.8610.05560.3352-0.2225-0.0660.00340.10850.0386-0.0605-0.03920.1820.0080.0070.3791-0.02130.2242-39.3806-9.5228-30.6856
25.0014-0.20460.03483.62130.92745.9655-0.29560.34620.1440.23990.00910.0841-0.6291-0.00220.19720.3260.0087-0.11690.25050.04570.2717-74.22913.5773-24.6482
34.9984-1.2059-1.34854.12392.11154.3647-0.0756-0.2626-0.32890.21-0.0724-0.10150.19730.1460.12760.1731-0.0136-0.00690.32720.07740.1667-40.2644-8.6318-9.007
46.57121.64562.93542.8241.16216.86120.07860.17350.04450.02570.0530.2050.1718-0.041-0.10580.15980.04910.00470.1944-0.01510.2357-72.1617-9.1795-14.2387
55.62181.86721.15185.81394.87344.6114-0.0237-0.7543-0.53721.95410.4426-1.12841.41581.4704-0.74260.71030.162-0.08520.65690.09210.6409-23.7428-18.8183-12.274
63.06981.94340.98713.0049-1.4572.89570.23450.12580.387-0.3170.1952-0.41160.29430.6696-0.33770.31960.05710.03510.55260.00560.3467-19.3142-16.2768-29.3126
74.17290.69780.08790.9175-0.39122.18170.03970.014-0.23760.0382-0.1022-0.0970.03120.09920.05040.20220.04510.01590.5469-0.02370.2384-117.3365-7.4156-43.0072
84.40940.47820.19933.9253-0.40584.2745-0.20490.13860.3083-0.14960.0767-0.0267-0.7488-0.04570.09370.39450.0408-0.13750.49670.0730.2689-82.6097.1338-44.2811
94.68812.2877-1.06514.0538-0.73562.724-0.09820.50240.032-0.23320.0782-0.0080.0114-0.18530.03360.22620.0569-0.00220.5932-0.02150.2063-116.49390.8579-63.1724
106.7838-3.0062.76924.4888-2.69556.0980.10660.409-0.2767-0.15040.1156-0.12070.4120.1083-0.21030.2349-0.0491-0.03540.4917-0.02770.2387-84.6763-1.4912-58.2925
116.19522.63522.41956.0875-3.11625.2709-0.19710.89440.3157-1.35430.25551.03010.18-1.29190.04640.540.0191-0.05991.0424-0.13090.4453-133.09-9.7626-63.3488
129.15811.5523-7.19462.7032-1.81545.79660.1356-0.0148-0.008-0.0040.06430.440.0470.7063-0.06480.3905-0.0605-0.02940.5154-0.10280.3307-137.4502-13.3218-46.4833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 121 )
2X-RAY DIFFRACTION2chain 'H' and (resid 122 through 226 )
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 107 )
4X-RAY DIFFRACTION4chain 'L' and (resid 108 through 211 )
5X-RAY DIFFRACTION5chain 'P' and (resid 164 through 175 )
6X-RAY DIFFRACTION6chain 'P' and (resid 176 through 185 )
7X-RAY DIFFRACTION7chain 'X' and (resid 1 through 121 )
8X-RAY DIFFRACTION8chain 'X' and (resid 122 through 225 )
9X-RAY DIFFRACTION9chain 'Y' and (resid 2 through 107 )
10X-RAY DIFFRACTION10chain 'Y' and (resid 108 through 211 )
11X-RAY DIFFRACTION11chain 'Z' and (resid 164 through 175 )
12X-RAY DIFFRACTION12chain 'Z' and (resid 176 through 185 )

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