[English] 日本語
Yorodumi
- PDB-5wjo: Crystal structure of the unliganded PG90 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wjo
TitleCrystal structure of the unliganded PG90 TCR
Components
  • PG90 TCR alpha chain
  • PG90 TCR beta chain
KeywordsIMMUNE SYSTEM / T Cell Receptor / heterodimer.
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShahine, A. / Gras, S. / Rossjohn, J.
CitationJournal: Sci Immunol / Year: 2017
Title: A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.
Authors: Shahine, A. / Van Rhijn, I. / Cheng, T.Y. / Iwany, S. / Gras, S. / Moody, D.B. / Rossjohn, J.
History
DepositionJul 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: 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.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PG90 TCR alpha chain
B: PG90 TCR beta chain
C: PG90 TCR alpha chain
D: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89920
Polymers101,2624
Non-polymers63616
Water6,503361
1
A: PG90 TCR alpha chain
B: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,94310
Polymers50,6312
Non-polymers3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-76 kcal/mol
Surface area20580 Å2
MethodPISA
2
C: PG90 TCR alpha chain
D: PG90 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95610
Polymers50,6312
Non-polymers3248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-77 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 128.080, 169.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein PG90 TCR alpha chain


Mass: 22839.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Protein PG90 TCR beta chain


Mass: 27791.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

-
Non-polymers , 4 types, 377 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 % / Description: Single rod shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 0.2M Magnesium Formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→39.18 Å / Num. obs: 32046 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.0129 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3558 / CC1/2: 0.607 / Rpim(I) all: 0.0567 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DXA, 1MI5

3dxa

1mi5


Resolution: 2.5→39.18 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.27 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1625 5.07 %RANDOM
Rwork0.208 ---
obs0.209 32046 100 %-
Displacement parametersBiso mean: 37.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.8034 Å20 Å20 Å2
2---3.1822 Å20 Å2
3----1.6212 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.5→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 28 365 7184
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077052HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039598HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3194SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes191HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1023HARMONIC5
X-RAY DIFFRACTIONt_it7052HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7814SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.305 130 4.44 %
Rwork0.243 2797 -
all0.246 2927 -
obs--99.97 %
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)
10.5399-0.29210.33790.21690.18240-0.00620.0331-0.04280.0131-0.0087-0.0131-0.0274-0.02890.0149-0.0295-0.03790.0131-0.0026-0.0226-0.015216.895926.9472-40.3168
20.7968-0.24940.220.24620.45580.073-0.02560.00190.0060.0252-0.0048-0.00380.0149-0.0250.0304-0.0025-0.00940.03-0.0197-0.0098-0.028431.17131.3299-27.6182
30.420.0850.03900.29290.59570.011-0.0080.0284-0.0096-0.0005-0.0221-0.01340.0171-0.0104-0.04110.00430.02830.0352-0.043-0.045227.6768-17.5088-6.894
40.19910.08290.12830.31980.20870.23620.02170.00670.0513-0.02310.0150.0113-0.0398-0.0037-0.0367-0.0178-0.01140.0611-0.0047-0.0605-0.001713.5024-4.1105-5.8046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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