[English] 日本語
Yorodumi
- PDB-9bp1: Rhesus macaque ITS110.01 Fab in complex with SIV Env MPER peptide -

+
Open data


ID or keywords:

Loading...

-
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 / viral envelope / symbiont entry into host cell / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more