[English] 日本語
Yorodumi
- PDB-3tpu: 42F3 p5E8/H2-Ld complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tpu
Title42F3 p5E8/H2-Ld complex
Components
  • 42F3 alpha
  • 42F3 beta
  • H2-Ld SBM2
  • p5E8 peptide
KeywordsIMMUNE SYSTEM / IG MHC / Antigen Recognition / TCR-pMHC / chimera protein / Membrane Receptor
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAdams, J.J. / Kranz, D.M. / Garcia, K.C.
CitationJournal: Immunity / Year: 2011
Title: T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.
Authors: Adams, J.J. / Narayanan, S. / Liu, B. / Birnbaum, M.E. / Kruse, A.C. / Bowerman, N.A. / Chen, W. / Levin, A.M. / Connolly, J.M. / Zhu, C. / Kranz, D.M. / Garcia, K.C.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: 42F3 alpha
B: 42F3 beta
I: H2-Ld SBM2
J: p5E8 peptide
C: 42F3 alpha
D: 42F3 beta
E: H2-Ld SBM2
F: p5E8 peptide
G: 42F3 alpha
H: 42F3 beta
K: H2-Ld SBM2
L: p5E8 peptide
M: 42F3 alpha
N: 42F3 beta
Q: H2-Ld SBM2
R: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,77832
Polymers291,27516
Non-polymers1,50316
Water724
1
A: 42F3 alpha
B: 42F3 beta
I: H2-Ld SBM2
J: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2038
Polymers72,8194
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 42F3 alpha
D: 42F3 beta
E: H2-Ld SBM2
F: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1077
Polymers72,8194
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 42F3 alpha
H: 42F3 beta
K: H2-Ld SBM2
L: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2999
Polymers72,8194
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: 42F3 alpha
N: 42F3 beta
Q: H2-Ld SBM2
R: p5E8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1698
Polymers72,8194
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)291.332, 291.332, 291.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11K-181-

SO4

21N-242-

SO4

31N-242-

SO4

-
Components

-
Protein , 2 types, 8 molecules BDHNIEKQ

#2: Protein
42F3 beta


Mass: 27248.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#3: Protein
H2-Ld SBM2


Mass: 21072.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS

-
Antibody / Protein/peptide , 2 types, 8 molecules ACGMJFLR

#1: Antibody
42F3 alpha


Mass: 23326.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#4: Protein/peptide
p5E8 peptide


Mass: 1171.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: GenScript

-
Non-polymers , 3 types, 20 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.4
Details: 1.1M lithium sulfate, 1% (v/v) PEG 200 and 0.1M sodium acetate pH 4.4, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→84.07 Å / Num. all: 104323 / Num. obs: 104323 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3.06 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFK

3tfk


Resolution: 3.1→45.313 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 4271 5.01 %random
Rwork0.2309 ---
all0.2322 85599 --
obs0.2322 85334 99.69 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.394 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8366 Å2-0 Å20 Å2
2---7.8366 Å2-0 Å2
3---26.1993 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20065 0 79 4 20148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01520684
X-RAY DIFFRACTIONf_angle_d1.55528074
X-RAY DIFFRACTIONf_dihedral_angle_d17.0387391
X-RAY DIFFRACTIONf_chiral_restr0.0932892
X-RAY DIFFRACTIONf_plane_restr0.0093669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.13530.35591570.34412580X-RAY DIFFRACTION96
3.1353-3.17210.33641460.31662625X-RAY DIFFRACTION98
3.1721-3.21080.28241300.31022664X-RAY DIFFRACTION99
3.2108-3.25150.33991360.30032662X-RAY DIFFRACTION100
3.2515-3.29420.31641390.29792714X-RAY DIFFRACTION100
3.2942-3.33930.35451320.29652663X-RAY DIFFRACTION100
3.3393-3.3870.33111530.28762683X-RAY DIFFRACTION100
3.387-3.43760.35191210.27922695X-RAY DIFFRACTION100
3.4376-3.49130.3331460.282698X-RAY DIFFRACTION100
3.4913-3.54850.30651510.272698X-RAY DIFFRACTION100
3.5485-3.60960.29531350.27852726X-RAY DIFFRACTION100
3.6096-3.67530.2861440.26032681X-RAY DIFFRACTION100
3.6753-3.74590.29131460.25132705X-RAY DIFFRACTION100
3.7459-3.82230.28821380.24542684X-RAY DIFFRACTION100
3.8223-3.90540.29671400.22942692X-RAY DIFFRACTION100
3.9054-3.99620.26151280.22222730X-RAY DIFFRACTION100
3.9962-4.09610.27171510.21512672X-RAY DIFFRACTION100
4.0961-4.20670.22211320.20382740X-RAY DIFFRACTION100
4.2067-4.33040.20371390.19192704X-RAY DIFFRACTION100
4.3304-4.47010.20931410.18932694X-RAY DIFFRACTION100
4.4701-4.62970.19171480.17052730X-RAY DIFFRACTION100
4.6297-4.81490.19341380.18132685X-RAY DIFFRACTION100
4.8149-5.03370.22871480.20432727X-RAY DIFFRACTION100
5.0337-5.29880.24851250.20882738X-RAY DIFFRACTION100
5.2988-5.63020.26251360.21772722X-RAY DIFFRACTION100
5.6302-6.06390.23151520.21372728X-RAY DIFFRACTION100
6.0639-6.67250.23431490.22072728X-RAY DIFFRACTION100
6.6725-7.6340.24581460.20422730X-RAY DIFFRACTION100
7.634-9.6030.20551670.19072750X-RAY DIFFRACTION100
9.603-45.3180.27051570.2642815X-RAY DIFFRACTION99

+
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