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- PDB-9bns: Rhesus macaque ITS114.01 Fab in complex with SIV MPER peptide -

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Basic information

Entry
Database: PDB / ID: 9bns
TitleRhesus macaque ITS114.01 Fab in complex with SIV MPER peptide
Components
  • ITS114 Heavy Chain
  • ITS114 Light Chain
  • MPER peptide
KeywordsIMMUNE SYSTEM / Fab / MPER / membrane-proximal external region / HIV-1 / gp41 / SIV
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGorman, J. / Lai, Y.-T. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2025
Title: Isolation and structure of broad SIV-neutralizing antibodies reveal a proximal helical MPER epitope recognized by a rhesus multi-donor class.
Authors: Gorman, J. / Du, R. / Lai, Y.T. / Ahmadi, M.S. / King, H.A.D. / Song, K. / Manalang, K. / Gonelli, C.A. / Schramm, C.A. / Cheng, C. / Nguyen, R. / Ambrozak, D. / Druz, A. / Shen, C.H. / ...Authors: Gorman, J. / Du, R. / Lai, Y.T. / Ahmadi, M.S. / King, H.A.D. / Song, K. / Manalang, K. / Gonelli, C.A. / Schramm, C.A. / Cheng, C. / Nguyen, R. / Ambrozak, D. / Druz, A. / Shen, C.H. / Yang, Y. / Douek, D.C. / Kwong, P.D. / Roederer, M. / Mason, R.D.
History
DepositionMay 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: MPER peptide
H: ITS114 Heavy Chain
L: ITS114 Light Chain
A: ITS114 Heavy Chain
B: ITS114 Light Chain
D: MPER peptide


Theoretical massNumber of molelcules
Total (without water)103,0916
Polymers103,0916
Non-polymers00
Water00
1
C: MPER peptide
H: ITS114 Heavy Chain
L: ITS114 Light Chain


Theoretical massNumber of molelcules
Total (without water)51,5463
Polymers51,5463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-20 kcal/mol
Surface area12820 Å2
MethodPISA
2
A: ITS114 Heavy Chain
B: ITS114 Light Chain
D: MPER peptide


Theoretical massNumber of molelcules
Total (without water)51,5463
Polymers51,5463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-30 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.900, 175.900, 205.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein/peptide MPER peptide


Mass: 4455.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus
#2: Antibody ITS114 Heavy Chain


Mass: 23717.758 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)
#3: Antibody ITS114 Light Chain


Mass: 23372.775 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)
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: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→44.44 Å / Num. obs: 36532 / % possible obs: 96.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 89.84 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.33
Reflection shellResolution: 3→3.07 Å / Num. unique obs: 5184 / CC1/2: 0.194

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Processing

Software
NameVersionClassification
PHENIXdev_5278refinement
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.44 Å / SU ML: 0.4849 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.5271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2709 1825 5 %
Rwork0.2282 34707 -
obs0.2304 36532 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.18 Å2
Refinement stepCycle: LAST / Resolution: 3→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 0 0 5578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235729
X-RAY DIFFRACTIONf_angle_d0.56187798
X-RAY DIFFRACTIONf_chiral_restr0.044868
X-RAY DIFFRACTIONf_plane_restr0.0091988
X-RAY DIFFRACTIONf_dihedral_angle_d13.66152050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.41391400.35942662X-RAY DIFFRACTION96.79
3.08-3.170.38991390.34382638X-RAY DIFFRACTION96.69
3.17-3.270.37261400.33362646X-RAY DIFFRACTION96.67
3.27-3.390.33941400.2942672X-RAY DIFFRACTION96.77
3.39-3.530.29441400.24642651X-RAY DIFFRACTION96.47
3.53-3.690.30371390.22862643X-RAY DIFFRACTION96.36
3.69-3.880.2861390.22782650X-RAY DIFFRACTION95.91
3.88-4.120.24681390.2152653X-RAY DIFFRACTION95.85
4.12-4.440.24071420.17782672X-RAY DIFFRACTION95.68
4.44-4.890.22081390.18392660X-RAY DIFFRACTION95.14
4.89-5.60.22831410.19322673X-RAY DIFFRACTION94.75
5.6-7.040.28851420.23192694X-RAY DIFFRACTION94.16
7.05-44.440.25281450.23132793X-RAY DIFFRACTION92.04
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)
12.80806462318-0.2501707091050.2101837011686.5369463045-1.543151092865.292311910310.492460077272-0.550494071395-0.8987209982570.1512677852030.3087099808530.5150285187981.392974363670.388120547453-0.8252486234150.8444099869610.0248438531952-0.3557549869230.800279670049-0.0261804810691.044524347862.474811048-94.2433613965-4.1881635463
24.969327416631.064930064623.789910870652.7105315162-0.7081043172854.934690174610.3867814395260.2960138698560.08348054268360.1317778246870.118867951817-0.2257031433160.2030499855451.58686184324-0.4905209627350.5711395190930.101370875957-0.08477007945261.53705319411-0.387691119930.94792458684279.4440948231-80.59985489140.124494685148
32.44167815495-0.787165201619-2.708273334344.871784260972.827912547877.285623945660.187119214609-0.179307316955-0.0917002427-0.03086570697150.0625402946546-0.346410883442-0.443749510847-0.177029878763-0.2360701351140.37955089694-0.1197057506670.03892891503730.7210521508120.06763808255380.77189611265935.5067426876-59.48969358553.84218113124
45.774243820880.740103751066-0.1205729663774.8931168577-2.200151842029.15349971433-0.170789956310.22559240511-0.5872232236960.2234877295330.1531828953290.037642188888-0.229842364468-1.12128075553-0.1025175677970.607300693801-0.0299051420092-0.005581346495091.03211133041-0.05892744456140.49727051736520.8658949187-58.529020760532.3191834362
57.575190503712.5443406908-3.464257679082.073423847510.5010623328874.66009160562-0.1001921314310.000859899835133-0.202247645740.128451339302-0.2563012578990.2129535892460.67431329571-1.717713742150.3135846102140.575629501869-0.2811932089270.04877804869261.32890142528-0.03477484741060.71623485022917.4046748931-72.71122143531.32992671415
62.809420861781.42803456184-0.165041216495.749461537111.48012757513.44126723798-0.2579398256360.0528478619469-0.1397071832480.154637806505-0.3987042840851.2291812084-0.424568682179-1.732696019470.6282026230760.6725642436190.1216691223460.0300760211541.76725896003-0.1738235955150.9620161057594.99290836549-55.569979080832.2361137444
77.69992506551-0.5376535919835.601350278342.32013505074-1.740355539937.394858746590.4909448832780.242962668402-1.10487397605-0.42288855384-0.8020920190760.5223998979510.5926486344140.9468609517370.2102826867690.443631373819-0.0242741331286-0.09345703005830.7302192426820.02318192035970.83067928921457.8508132595-79.9716298235-16.2167732028
82.965922669352.46880747842-0.433802162842.05152341265-0.355516816860.06012252011430.4346988873180.0137672371354-0.6444929437180.049529617135-0.1681160117380.6532420796911.66784523688-3.0475020560.2206540166670.718510664351-0.728161982527-0.01821306441831.660575585810.2257834592691.1785260690439.1974327181-84.0846977362-11.9727331441
97.28213275792-4.49529918137-2.640585269285.930537930140.5912620486026.949564561410.03830700656860.3583203524110.075660396358-0.006242494122680.002551563996740.276507131931-0.81141870533-0.1818623009950.02647438275670.542425399459-0.160586977920.08252079024470.625543995905-0.05808358172470.77272112479740.2559774758-67.1325444836-12.418037451
105.67923402219-4.97647831553-5.175834376447.131695566714.169075106174.785782405740.07319378363560.3327987313021.234106526420.3459172023971.1795855335-0.436348711205-0.8794147375471.78335892614-1.21016001390.556651666533-0.1758839002640.1514275759640.995115119012-0.1079593763911.0012352156656.6496733686-64.2353943582-12.5807357765
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 115 )HB1 - 1151 - 125
22chain 'L' and (resid 1 through 106 )LC1 - 1061 - 106
33chain 'A' and (resid 1 through 114 )AD1 - 1141 - 124
44chain 'A' and (resid 115 through 212)AD115 - 212125 - 222
55chain 'B' and (resid 1 through 110 )BE1 - 1101 - 110
66chain 'B' and (resid 111 through 214 )BE111 - 214111 - 214
77chain 'C' and (resid 660 through 672 )CA660 - 6721 - 13
88chain 'C' and (resid 673 through 684 )CA673 - 68414 - 25
99chain 'D' and (resid 660 through 672 )DF660 - 6721 - 13
1010chain 'D' and (resid 673 through 685 )DF673 - 68514 - 26

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