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- PDB-9bp1: Rhesus macaque ITS110.01 Fab in complex with SIV Env MPER peptide -

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Basic information

Entry
Database: PDB / ID: 9bp1
TitleRhesus macaque ITS110.01 Fab in complex with SIV Env MPER peptide
Components
  • Envelope glycoprotein gp160
  • ITS110.01 Heavy Chain
  • ITS110.01 Light Chain
KeywordsIMMUNE SYSTEM/Viral protein / Fab / MPER / membrane-proximal external region / HIV-1 / gp41 / IMMUNE SYSTEM / SIV / antibody / IMMUNE SYSTEM-Viral protein complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsGorman, J. / 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 6, 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
A: ITS110.01 Heavy Chain
B: ITS110.01 Light Chain
I: Envelope glycoprotein gp160
E: Envelope glycoprotein gp160
H: ITS110.01 Heavy Chain
D: ITS110.01 Light Chain


Theoretical massNumber of molelcules
Total (without water)102,5786
Polymers102,5786
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-39 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.174, 210.174, 46.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62

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Components

#1: Antibody ITS110.01 Heavy Chain


Mass: 24467.344 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 ITS110.01 Light Chain


Mass: 23375.912 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: Protein/peptide Envelope glycoprotein gp160


Mass: 3445.951 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus / References: UniProt: A0A4Y5TJX4
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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 22% PEG8000 .1M Tris pH8.5

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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: 3.58→40 Å / Num. obs: 13619 / % possible obs: 95.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 42.46 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.094 / Rrim(I) all: 0.17 / Χ2: 0.859 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.58-3.6620.9696150.3580.7260.7931.2591.13188.7
3.66-3.732.20.836280.3840.7450.6571.0640.95991
3.73-3.82.40.8976500.3850.7460.6761.1291.04190.9
3.8-3.882.60.7756550.4480.7870.5580.9590.94492.3
3.88-3.962.70.7326760.5710.8530.5170.9011.00499.6
3.96-4.052.80.5456930.6930.9050.3730.6630.97398.9
4.05-4.162.90.4776880.7750.9350.3280.5810.99594.8
4.16-4.2730.3846600.840.9550.2590.4650.92494.7
4.27-4.3930.3376850.8420.9560.2270.4080.93799.9
4.39-4.5330.2667150.880.9680.1790.3220.92999
4.53-4.73.20.2216610.9270.9810.1470.2660.91693.5
4.7-4.883.10.1886930.9130.9770.1270.2280.822100
4.88-5.113.10.1816920.9370.9840.1220.2190.86395.7
5.11-5.373.20.1536880.9380.9840.1020.1850.81497.7
5.37-5.713.10.1456940.9310.9820.0960.1750.77896.9
5.71-6.153.20.1376890.9380.9840.0890.1640.78197
6.15-6.773.10.1146950.9670.9910.0730.1350.73395.3
6.77-7.743.10.0927050.9730.9930.0590.1090.62796
7.74-9.733.10.0887070.9740.9930.0540.1040.64997
9.73-402.90.0897300.9590.9890.0590.1070.72494

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Processing

Software
NameVersionClassification
PHENIXdev_5278refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→39.72 Å / SU ML: 0.4508 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 605 5 %
Rwork0.2202 11483 -
obs0.2226 12088 84.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.5 Å2
Refinement stepCycle: LAST / Resolution: 3.58→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6817 0 0 0 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166980
X-RAY DIFFRACTIONf_angle_d0.44069512
X-RAY DIFFRACTIONf_chiral_restr0.04181088
X-RAY DIFFRACTIONf_plane_restr0.00371207
X-RAY DIFFRACTIONf_dihedral_angle_d11.96942464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.940.3949930.27751771X-RAY DIFFRACTION53.29
3.94-4.50.2461650.22683142X-RAY DIFFRACTION94
4.51-5.670.25621720.19973251X-RAY DIFFRACTION96.26
5.67-39.720.24581750.20733319X-RAY DIFFRACTION95.05
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)
10.0875917292557-0.0375817242266-0.002527250123180.0181870433936-0.002999008791620.2109742576780.286561146534-0.1037592606690.0268974951482-0.09421772351440.2298716825390.159567325291-0.14045756477-0.4338348676520.6450072906130.2407074797990.1320481893460.05919061471010.7879134592850.7040422270090.3045188530362.4976752923-66.8408327676-8.10439268099
20.2008892601310.06329424696420.06037415532750.03226520696780.0180173070680.0158796490247-0.2326844035880.0577813733371-0.1331276344220.2181582749220.1914407696040.0978278173686-0.0515193581893-0.0303102034307-0.04251206195220.1540069297750.1514432733290.2894073451370.0357277055789-0.02720593341310.075519654250174.8717129403-42.2065049166-31.2312515731
30.0923728556779-0.0828214380573-0.03505432144350.06322523070910.02646905277780.04631289766670.1721800147130.0395028533460.114063955058-0.2126145048530.1616453940290.0426175648848-0.0543414211766-0.2208511216860.3149876967320.0998703769063-0.1472261160290.0924720594036-0.1114069138440.25739519205-0.07007462605183.1775634455-72.9858890546-12.929264965
40.0839458385204-0.01186599737310.05426850673870.107691328521-0.07812444686240.0850912995911-0.139276113975-0.0381003933711-0.01284564797370.0916827877005-0.0118020040723-0.0303008232281-0.2402969809450.0143201119588-0.4037492898660.3548863495450.1059301340650.00218958969253-0.04236131096910.238650290855-0.29315412238688.7321525772-39.2930408648-24.0691102316
50.0066505027360.00273451384704-0.0100326930330.0219891168643-0.03024411416060.0505296779819-0.003959713471060.02164736620870.0003586313938030.0555014683732-0.01429477679530.019494926285-0.0597770206222-0.0584826332024-0.04854718665920.311573799556-0.03008857483640.006695079674510.4882259645680.3648602140960.29116297906162.3286856454-81.7400259142.38731811069
60.000456523018640.0002566357425340.0006257293467130.0008339450290020.002000320296780.006667807194780.001042559180710.0218180931482-0.00422429951283-0.02182216947540.000564925973909-0.0106474077192-0.0310770918519-0.0106803676734-0.00136190116310.3089422048660.03011168223720.02116320165220.687179994388-0.4448829834740.54812948638943.8054268643-79.2453820621.27096611371
70.0564727361840.0109183454824-0.004024040551180.0192538554143-0.004928254454780.0137908184993-0.01084712169680.185402281109-0.04266503948970.0406370474599-0.1087510897360.0951116148362-0.0195723769986-0.0768628348822-0.115766155158-0.127914798286-0.0761339697210.2605450432641.0753338343-0.6391689726560.83601964879447.2046099122-64.528242958511.7076794114
80.01885091863380.0101008540566-0.00701213034144-0.0029272612752-0.0045116885290.0141835521189-0.0138901952999-0.01218823525920.008028987088440.1216677584830.006570120347190.0735789726010.01622174241770.1053753844890.01327791760730.335542823942-0.007259232036430.6014875913910.493870127609-0.3534652116110.64041447331441.6527359898-37.842644756634.4426378162
90.0691367720217-0.007775625976860.02017273571940.02367041469380.01794584199290.03059759987630.1031301660680.155421754984-0.00135261674370.003045510612060.1111997321180.0120487400845-0.06605249355860.0683952982470.09965209583310.0328540955516-0.166853952740.3085510230720.719685670202-0.400240980290.78497507625825.5492071295-65.15450802316.6327658771
100.143400536466-0.05841079232660.06879919537820.0262179863354-0.01985255921410.0685385707357-0.05181294588540.002452275380180.1209861337350.000629852545453-0.125394613723-0.0304839218512-0.0175212253350.0148503048811-0.1650300047450.575913289170.3003489945980.4534076443140.914743263213-0.2498859282521.3741258722229.0048589641-31.209234714427.3548992311
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 109 )AA1 - 1091 - 119
22chain 'A' and (resid 110 through 214 )AA110 - 214120 - 224
33chain 'B' and (resid 1 through 110 )BB1 - 1101 - 110
44chain 'B' and (resid 111 through 212 )BB111 - 212111 - 212
55chain 'I' and (resid 660 through 675 )IC660 - 6751 - 16
66chain 'E' and (resid 660 through 675 )ED660 - 6751 - 16
77chain 'H' and (resid 1 through 109 )HE1 - 1091 - 119
88chain 'H' and (resid 110 through 210 )HE110 - 210120 - 220
99chain 'D' and (resid 1 through 110 )DF1 - 1101 - 110
1010chain 'D' and (resid 111 through 210 )DF111 - 210111 - 210

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