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- PDB-8fbw: Crystal structure of SIV-1 V2 antibody NCI05 in complex with a V2... -

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Basic information

Entry
Database: PDB / ID: 8fbw
TitleCrystal structure of SIV-1 V2 antibody NCI05 in complex with a V2 peptide
Components
  • Heavy chain of anti-SIV V2 antibody NCI05
  • Light chain of anti-SIV V2 antibody NCI05
  • SIV V2 peptide
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SIV / antibody / NCI05 / V2 / variable loop 2 / SIVmac251 / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhou, T. / Kwong, P.D. / Van Wazer, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Virol. / Year: 2023
Title: Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or beta-Sheet Conformations on Time of SIV mac251 Acquisition.
Authors: Stamos, J.D. / Rahman, M.A. / Gorini, G. / Silva de Castro, I. / Becerra-Flores, M. / Van Wazer, D.J. / N'Guessan, K.F. / Clark, N.M. / Bissa, M. / Gutowska, A. / Mason, R.D. / Kim, J. / ...Authors: Stamos, J.D. / Rahman, M.A. / Gorini, G. / Silva de Castro, I. / Becerra-Flores, M. / Van Wazer, D.J. / N'Guessan, K.F. / Clark, N.M. / Bissa, M. / Gutowska, A. / Mason, R.D. / Kim, J. / Rao, M. / Roederer, M. / Paquin-Proulx, D. / Evans, D.T. / Cicala, C. / Arthos, J. / Kwong, P.D. / Zhou, T. / Cardozo, T. / Franchini, G.
History
DepositionNov 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Heavy chain of anti-SIV V2 antibody NCI05
D: Light chain of anti-SIV V2 antibody NCI05
E: SIV V2 peptide
A: Heavy chain of anti-SIV V2 antibody NCI05
B: Light chain of anti-SIV V2 antibody NCI05
F: SIV V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,91512
Polymers99,2706
Non-polymers1,6456
Water4,756264
1
C: Heavy chain of anti-SIV V2 antibody NCI05
D: Light chain of anti-SIV V2 antibody NCI05
E: SIV V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7617
Polymers49,6353
Non-polymers1,1264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-18 kcal/mol
Surface area21460 Å2
MethodPISA
2
A: Heavy chain of anti-SIV V2 antibody NCI05
B: Light chain of anti-SIV V2 antibody NCI05
F: SIV V2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1545
Polymers49,6353
Non-polymers5192
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-22 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.650, 130.650, 216.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide SIV V2 peptide


Mass: 2179.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus

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Antibody , 2 types, 4 molecules CADB

#1: Antibody Heavy chain of anti-SIV V2 antibody NCI05


Mass: 24758.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody Light chain of anti-SIV V2 antibody NCI05


Mass: 22696.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 268 molecules

#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M sodium chloride, 28.5% PEG8000, 0.1 M phosphate/citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 46240 / % possible obs: 100 % / Redundancy: 22 % / Rmerge(I) obs: 0.119 / Χ2: 0.035 / Net I/σ(I): 24.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.3922.91.0622750.3261100
2.39-2.43120.89343290.3321100
2.43-2.4811.90.75842610.3421100
2.48-2.5311.80.68343400.3381100
2.53-2.5911.70.61542850.3451100
2.59-2.6511.50.54143180.3561100
2.65-2.71110.44543100.3871100
2.71-2.7910.20.35243280.4091100
2.79-2.8712.10.30942910.4241100
2.87-2.9612.30.26243230.4621100
2.96-3.0712.30.21442860.5031100
3.07-3.1912.20.18643460.5461100
3.19-3.3312.10.14743060.6061100
3.33-3.5111.90.11943050.7041100
3.51-3.7311.60.10243280.8021100
3.73-4.0210.60.08943000.8891100
4.02-4.42120.07143090.9551100
4.42-5.0612.60.06243170.9431100
5.06-6.3712.20.05743170.7471100
6.37-1011.50.04443440.7561100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487-000refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→48.91 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 2000 4.39 %
Rwork0.1941 --
obs0.1963 45518 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6948 0 107 264 7319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.554
X-RAY DIFFRACTIONf_dihedral_angle_d7.4391046
X-RAY DIFFRACTIONf_chiral_restr0.0431105
X-RAY DIFFRACTIONf_plane_restr0.0041246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.30431360.23422962X-RAY DIFFRACTION95
2.41-2.470.27071360.23282976X-RAY DIFFRACTION97
2.47-2.550.30081390.23072995X-RAY DIFFRACTION97
2.55-2.630.38631390.25293033X-RAY DIFFRACTION98
2.63-2.720.26261400.22653043X-RAY DIFFRACTION98
2.72-2.830.28871400.20783058X-RAY DIFFRACTION99
2.83-2.960.2871410.2133070X-RAY DIFFRACTION99
2.96-3.120.24991430.22043100X-RAY DIFFRACTION99
3.12-3.310.32141430.223114X-RAY DIFFRACTION100
3.31-3.570.24341450.19453153X-RAY DIFFRACTION100
3.57-3.930.24081450.18453160X-RAY DIFFRACTION100
3.93-4.50.19331470.15893189X-RAY DIFFRACTION100
4.5-5.660.18111490.16233249X-RAY DIFFRACTION100
5.66-48.910.25771570.19513416X-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)
10.2068-0.3129-0.04870.42450.23130.4434-0.0147-0.00130.0414-0.0053-0.02590.08020.1150.2017-00.22610.0338-0.0240.3916-0.03330.264349.8872-64.1499-15.5868
20.10270.04190.15630.10780.06780.3021-0.02730.06750.1834-0.0416-0.0233-0.0071-0.08310.114700.2371-0.0554-0.01150.3212-0.03110.334642.5295-39.19859.6972
30.0179-0.02890.05890.1103-0.16330.25340.0577-0.1768-0.0389-0.047-0.17530.17740.07920.0231-0.04940.205-0.0694-0.01640.3031-0.07030.33638.832-43.639316.7057
40.01940.01860.01630.02080.00880.0028-0.06450.11910.1381-0.2170.1083-0.0202-0.4090.1496-00.6372-0.00230.00640.44910.0710.519845.5144-40.3986-27.946
50.05240.01820.01180.3134-0.15060.24430.05190.14020.073-0.3888-0.01010.1513-0.26980.11970.00010.41330.0241-0.03390.41160.070.327842.8772-50.2406-28.0582
60.0212-0.01450.0269-0.0003-0.00220.0145-0.11720.0169-0.0358-0.00030.2041-0.0602-0.1498-0.0776-0.00010.48560.0528-0.04440.43160.05880.38539.2315-33.1472-16.3055
70.267-0.2259-0.15550.26940.13660.12620.04390.04170.0281-0.0085-0.00790.0131-0.3436-0.034700.4006-0.07030.00210.32160.0030.278848.6697-28.5125.9585
80.0273-0.0325-0.00130.03770.00530.0039-0.0081-0.00840.1114-0.1317-0.05070.064-0.0594-0.040400.75840.03750.00430.3573-0.02340.28544.5535-20.796510.6501
90.0045-0.00010.0096-0.0004-0.00070.00020.12010.07240.0184-0.22720.35360.032-0.08550.199-0.00010.49530.104-0.02190.6426-0.04440.338457.245-70.8887-27.6439
100.0045-0.0003-0.00430.0027-0.0030.00380.04770.0077-0.04870.0505-0.00650.0085-0.01170.031100.7320.1549-0.25970.6183-0.07790.539252.6974-83.0468-28.2697
110.0541-0.09860.01460.2322-0.35891.0991-0.2028-0.44590.7295-0.06280.0787-0.045-0.2765-0.59160.02710.3780.09-0.00830.6163-0.1980.928912.2682-29.238510.2264
120.09380.0648-0.17550.30160.12320.7501-0.0076-0.1140.6999-0.0643-0.0455-0.23480.0309-0.5747-0.0750.18380.0364-0.02440.5858-0.00860.904314.1807-31.19945.1427
130.3075-0.1692-0.26430.43-0.19720.66660.0947-0.2113-0.2329-0.2633-0.1631-0.02470.5612-0.17190.03990.4218-0.20240.05940.46010.03450.354728.4948-69.8231.2579
140.0535-0.05260.02540.3239-0.05360.41840.0557-0.07060.14440.1445-0.0824-0.12690.2498-0.29040.0090.2639-0.11490.01740.529-0.04910.339927.6956-60.02086.8684
150.03080.02430.02320.01150.00450.0133-0.23220.00250.1648-0.0658-0.2533-0.0196-0.2046-0.1234-00.49120.0633-0.06290.9959-0.01470.89197.5156-36.1766-17.3805
160.06060.0253-0.03710.0235-0.04180.1537-0.16220.12490.1818-0.3155-0.02780.2769-0.4220.0301-0.08310.60610.2496-0.14320.59460.12510.929713.8328-26.6082-11.4714
170.1016-0.0405-0.090.1553-0.08360.1634-0.1120.09830.4902-0.1643-0.20020.4154-0.1999-0.2635-0.04670.49890.2417-0.10150.87260.05741.079.8396-29.9589-12.5457
180.03780.0107-0.05130.1249-0.08410.1298-0.0498-0.0590.2078-0.0434-0.15160.05640.2252-0.07780.00320.2592-0.01110.05110.76820.0970.547216.8268-48.2211-17.2075
190.379-0.48920.06170.5829-0.0988-0.00630.1417-0.02160.0951-0.0803-0.2289-0.18270.3642-0.26310.03390.3901-0.2334-0.04160.59270.03040.286718.2076-67.8669-1.4715
200.3216-0.00640.13970.01430.03220.17590.2021-0.42760.14090.1827-0.0015-0.12650.3101-0.55110.45190.0109-0.6781-0.2470.5968-0.03260.281814.5076-65.9868-2.2209
210.3385-0.1445-0.11090.1784-0.06320.11910.18840.0767-0.03210.1908-0.14530.00150.3871-0.25850.1110.635-0.2423-0.14330.444-0.01770.432516.7612-73.8599-7.9979
220.0004-0.00270.00350.0035-0.00360.00110.03830.0091-0.02720.1003-0.1265-0.0373-0.0699-0.0022-01.09790.21470.05890.84-0.20311.6422.6957-14.97527.2654
230.0014-0.0011-0.00020.0003-0.00020.00060.01850.00940.00210.00010.06130.00160.0071-0.025201.57710.12760.11741.6530.04941.30118.3135-5.734111.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 127 )
2X-RAY DIFFRACTION2chain 'C' and (resid 128 through 204 )
3X-RAY DIFFRACTION3chain 'C' and (resid 205 through 231 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 23 )
5X-RAY DIFFRACTION5chain 'D' and (resid 24 through 101 )
6X-RAY DIFFRACTION6chain 'D' and (resid 102 through 117 )
7X-RAY DIFFRACTION7chain 'D' and (resid 118 through 201 )
8X-RAY DIFFRACTION8chain 'D' and (resid 202 through 216 )
9X-RAY DIFFRACTION9chain 'E' and (resid 175 through 184 )
10X-RAY DIFFRACTION10chain 'E' and (resid 185 through 190 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 90 )
12X-RAY DIFFRACTION12chain 'A' and (resid 91 through 140 )
13X-RAY DIFFRACTION13chain 'A' and (resid 141 through 161 )
14X-RAY DIFFRACTION14chain 'A' and (resid 162 through 231 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1 through 23 )
16X-RAY DIFFRACTION16chain 'B' and (resid 24 through 62 )
17X-RAY DIFFRACTION17chain 'B' and (resid 63 through 101 )
18X-RAY DIFFRACTION18chain 'B' and (resid 102 through 117 )
19X-RAY DIFFRACTION19chain 'B' and (resid 118 through 154 )
20X-RAY DIFFRACTION20chain 'B' and (resid 155 through 191 )
21X-RAY DIFFRACTION21chain 'B' and (resid 192 through 214 )
22X-RAY DIFFRACTION22chain 'F' and (resid 175 through 184 )
23X-RAY DIFFRACTION23chain 'F' and (resid 185 through 189 )

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