[English] 日本語
Yorodumi
- PDB-8rd2: Trypanosoma brucei Invariant Surface Glycoprotein 75 (ISG75) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rd2
TitleTrypanosoma brucei Invariant Surface Glycoprotein 75 (ISG75)
ComponentsInvariant surface glycoprotein
KeywordsIMMUNOSUPPRESSANT / receptor / inhibitor / immunoglobulin / parasite / invariant
Function / homologyProteasome subunit Rpn10 / Trypanosome invariant surface glycoprotein / Invariant surface glycoprotein / proteasome regulatory particle, base subcomplex / ubiquitin-dependent protein catabolic process / membrane / Invariant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsStodkilde-Jorgensen, K. / Mikkelsen, J.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Other governmentAUFF-E-2015-FLS-8-64 Denmark
CitationJournal: J Immunol. / Year: 2024
Title: Trypanosoma brucei Invariant Surface Glycoprotein 75 Is an Immunoglobulin Fc Receptor Inhibiting Complement Activation and Antibody-Mediated Cellular Phagocytosis.
Authors: Mikkelsen, J.H. / Stodkilde, K. / Jensen, M.P. / Hansen, A.G. / Wu, Q. / Lorentzen, J. / Graversen, J.H. / Andersen, G.R. / Fenton, R.A. / Etzerodt, A. / Thiel, S. / Andersen, C.B.F.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invariant surface glycoprotein
B: Invariant surface glycoprotein


Theoretical massNumber of molelcules
Total (without water)98,4422
Polymers98,4422
Non-polymers00
Water00
1
A: Invariant surface glycoprotein


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invariant surface glycoprotein


Theoretical massNumber of molelcules
Total (without water)49,2211
Polymers49,2211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.010, 120.010, 107.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

#1: Protein Invariant surface glycoprotein


Mass: 49220.949 Da / Num. of mol.: 2 / Mutation: N134A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: Lister 427 / Gene: ISG75 / Production host: Komagataella pastoris (fungus) / Strain (production host): Superman5 / References: UniProt: Q26769

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350 100 mM HEPES pH 7.5 20 mM Sorbitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.69→53.67 Å / Num. obs: 22111 / % possible obs: 53.3 % / Redundancy: 4.65 % / Biso Wilson estimate: 82.72 Å2 / CC1/2: 0.9982 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.38
Reflection shellResolution: 2.7→3 Å / Rmerge(I) obs: 1.004 / Num. unique obs: 1106 / CC1/2: 0.5407 / % possible all: 10.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→53.67 Å / SU ML: 0.3787 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.8899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2721 1222 5.53 %
Rwork0.2284 20889 -
obs0.2308 22111 52.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.15 Å2
Refinement stepCycle: LAST / Resolution: 2.69→53.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 0 0 6261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226340
X-RAY DIFFRACTIONf_angle_d0.48138508
X-RAY DIFFRACTIONf_chiral_restr0.0331929
X-RAY DIFFRACTIONf_plane_restr0.00371120
X-RAY DIFFRACTIONf_dihedral_angle_d15.36322460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.80.2772130.3979237X-RAY DIFFRACTION5.36
2.8-2.920.4114250.4177489X-RAY DIFFRACTION11.03
2.92-3.080.3199610.3683871X-RAY DIFFRACTION19.91
3.08-3.270.3818800.33911314X-RAY DIFFRACTION29.89
3.27-3.520.35821210.33031942X-RAY DIFFRACTION43.54
3.52-3.880.33131870.27923178X-RAY DIFFRACTION71.55
3.88-4.440.28212350.23394037X-RAY DIFFRACTION90.64
4.44-5.590.27682460.22984410X-RAY DIFFRACTION97.59
5.59-53.670.22222540.18064411X-RAY DIFFRACTION97.05
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)
12.953488163120.06082577945840.8088866152773.922648490112.379001875576.946982049160.300094952348-0.003125718208950.217473575857-0.2155016121930.0294020649422-0.509360173488-0.002187905897310.707805071147-0.2527883475240.278754714892-0.1832867520560.04061336343120.3712143767640.1233074949990.3632125677722.6721642069-48.122871066514.8161325008
21.452676064761.112641921181.720473843981.138992353171.617193900562.20436381531-0.103438331451-0.7537818720520.2528975245510.024096331045-0.6541515803880.203778866668-0.144961916-0.9058600640670.7111694842690.5423856187150.152337778713-0.1190674911890.827529016061-0.2002774863260.580364242921-0.541576463592-44.786032585810.0959186408
34.715129070430.1231294916671.926312809771.99420426058-0.1881613208192.961095830320.024417245636-0.127391294221-0.386240920647-0.219369409602-0.4274977652140.1464770504170.8116495051260.02548417962380.03990914237050.550885340559-0.4693472606310.04883963074570.5609994231140.005415814159780.23745046430744.4517648019-26.3911970269-3.93367530563
43.39920604536-0.5385319799081.686140027950.673423182481-0.3107803007883.180972868470.2565839766491.01693845944-0.756134948915-0.178935684138-0.4159112003080.4027832026810.560193627742-0.827253960992-0.3665006781140.899331088015-0.887575894253-0.2643012778631.43566188111-0.2500133626420.79773085710517.9292465513-32.4844975891-27.1275705531
55.443380389070.424594948863-1.046080952592.922181049890.5174446612863.399028054290.0203025571877-1.1998829111-0.2642991926270.387292448794-0.01493617467140.5415475123980.351465171006-0.4790198273290.2236474605960.553279589417-0.4854090571840.1411922173810.649713620721-0.07867842431090.42429659862235.8739734056-23.13264517393.30305084701
68.30229142412.61039322382-2.199602833643.033562156951.950863801994.10057592879-0.0550065381865-1.30075732933-1.669027955520.2441009035660.238653272825-0.393257880651.33664632570.389857572535-0.02435706118750.619629011488-0.03894037562910.0796165820210.4283090465910.1594474899570.58668125764755.2137662174-30.8105225789-1.40681008127
70.9747890831420.473439554969-0.5177242070151.958069103740.5427610767923.00742386581-0.102496480150.634541920392-0.0430204500366-0.755057452170.1344891765480.728495913931-0.178987457275-1.089642320990.2407105810810.79772184764-0.724269297638-0.3183174658791.14395115103-0.2545250887670.75020862132518.813594646-23.3741155501-29.7934135857
81.69823007506-0.1404165419652.453231085441.8297782116-0.4253262355917.881980955450.133015094615-0.26048349820.2016625545130.0369129066645-0.06042519639480.372849636303-0.343707341915-0.889106390236-0.09124173154350.510327016015-0.1496734879650.1508463957460.899524752754-0.2536703194760.92025800031622.4778814356-9.12983501453.64228018467
91.468867190760.2316136397821.23305607042.08731890357-0.160196369355.442857348020.13505084866-0.3054612929350.177150519610.264581721573-0.04966869254390.4086879134730.242441037993-1.40962984331-0.1633153572130.464487689504-0.2311909825020.1105838052641.05099013497-0.1814934797210.97918351025721.6505459326-12.97196157910.8171548404
100.13187104315-0.1086672602980.4784097229971.42022485996-2.308321527364.474259987960.02313318124880.907306308590.162709376497-1.151143570720.1247858759080.01328969634970.0363470049003-0.4037309401570.06312885789541.34643138971-0.598667096859-0.1349986663491.46664142882-0.06641383308390.93550141042321.8626705092-21.0057043398-38.5917852632
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 291 )AA29 - 2911 - 254
22chain 'A' and (resid 292 through 435 )AA292 - 435255 - 398
33chain 'B' and (resid 29 through 63 )BB29 - 631 - 35
44chain 'B' and (resid 64 through 145 )BB64 - 14536 - 117
55chain 'B' and (resid 146 through 218 )BB146 - 218118 - 183
66chain 'B' and (resid 219 through 252 )BB219 - 252184 - 217
77chain 'B' and (resid 253 through 295 )BB253 - 295218 - 260
88chain 'B' and (resid 296 through 354 )BB296 - 354261 - 319
99chain 'B' and (resid 355 through 416 )BB355 - 416320 - 381
1010chain 'B' and (resid 417 through 435 )BB417 - 435382 - 400

+
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://pdbjlvh1.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