[English] 日本語
Yorodumi
- PDB-6j2f: Crystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j2f
TitleCrystal structure of bat (Pteropus Alecto) MHC class I Ptal-N*01:01 in complex with Hendra virus-derived peptide HeV2
Components
  • HeV2
  • Ptal-N*01:01
  • beta-2 microglobulin
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / host cell surface / immune response ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / host cell surface / immune response / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / signaling receptor binding / viral envelope / host cell plasma membrane / virion membrane / extracellular space / extracellular region / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / 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 / Beta-2-Microglobulin / : ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / 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 / Beta-2-Microglobulin / : / 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 / Nucleic acid-binding, OB-fold / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesPteropus alecto (black flying fox)
Hendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLu, D. / Liu, K.F. / Yue, C. / Lu, Q. / Cheng, H. / Chai, Y. / Qi, J.X. / Gao, G.F. / Liu, W.J.
CitationJournal: Plos Biol. / Year: 2019
Title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats.
Authors: Lu, D. / Liu, K. / Zhang, D. / Yue, C. / Lu, Q. / Cheng, H. / Wang, L. / Chai, Y. / Qi, J. / Wang, L.F. / Gao, G.F. / Liu, W.J.
History
DepositionJan 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title
Revision 1.2Dec 4, 2019Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ptal-N*01:01
B: beta-2 microglobulin
C: HeV2
D: Ptal-N*01:01
E: beta-2 microglobulin
F: HeV2


Theoretical massNumber of molelcules
Total (without water)89,2846
Polymers89,2846
Non-polymers00
Water11,169620
1
A: Ptal-N*01:01
B: beta-2 microglobulin
C: HeV2


Theoretical massNumber of molelcules
Total (without water)44,6423
Polymers44,6423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-19 kcal/mol
Surface area18450 Å2
MethodPISA
2
D: Ptal-N*01:01
E: beta-2 microglobulin
F: HeV2


Theoretical massNumber of molelcules
Total (without water)44,6423
Polymers44,6423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-16 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.245, 102.527, 176.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

-
Components

#1: Protein Ptal-N*01:01


Mass: 32119.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: Ptal-N / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A125R585
#2: Protein beta-2 microglobulin


Mass: 11474.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteropus alecto (black flying fox) / Gene: PAL_GLEAN10023531 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: L5K3Y9
#3: Protein/peptide HeV2


Mass: 1048.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Hendra virus / References: UniProt: O89342*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M ...Details: 0.075 M HEPES (pH 7.5), 15% (w/v) polyethylene glycol 10,000, and 25% (v/v) glycerol at a protein concentration of 10 mg/mL. Single crystals of Ptal-N*01:01/ EBOV-NP1 were grown in 0.1 M succinic acid pH 7.0, 15% w/v polyethylene glycol 3,350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 72225 / % possible obs: 100 % / Redundancy: 13.4 % / Net I/σ(I): 3.25
Reflection shellResolution: 2.3→2.38 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.839 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2308 3592 5.11 %
Rwork0.2026 --
obs0.2041 70243 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 0 620 6920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016506
X-RAY DIFFRACTIONf_angle_d1.1358866
X-RAY DIFFRACTIONf_dihedral_angle_d23.6072404
X-RAY DIFFRACTIONf_chiral_restr0.074890
X-RAY DIFFRACTIONf_plane_restr0.0081184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8928-1.91770.28491000.25031803X-RAY DIFFRACTION70
1.9177-1.9440.29351130.24442153X-RAY DIFFRACTION81
1.944-1.97180.26111480.23382200X-RAY DIFFRACTION85
1.9718-2.00120.28131370.23642402X-RAY DIFFRACTION92
2.0012-2.03250.26651190.23552496X-RAY DIFFRACTION96
2.0325-2.06580.25851480.23242551X-RAY DIFFRACTION97
2.0658-2.10140.24811240.22192649X-RAY DIFFRACTION100
2.1014-2.13960.24861530.22172581X-RAY DIFFRACTION100
2.1396-2.18080.23791270.22192655X-RAY DIFFRACTION100
2.1808-2.22530.25771540.22372602X-RAY DIFFRACTION100
2.2253-2.27370.24321290.22112635X-RAY DIFFRACTION100
2.2737-2.32650.25681750.21422595X-RAY DIFFRACTION100
2.3265-2.38470.24961490.21662641X-RAY DIFFRACTION100
2.3847-2.44920.2431530.21992610X-RAY DIFFRACTION100
2.4492-2.52120.24611580.22282597X-RAY DIFFRACTION100
2.5212-2.60260.26291430.22152637X-RAY DIFFRACTION100
2.6026-2.69560.27961200.22782668X-RAY DIFFRACTION100
2.6956-2.80350.25961360.22532630X-RAY DIFFRACTION100
2.8035-2.9310.21791360.21052666X-RAY DIFFRACTION100
2.931-3.08540.241340.20732648X-RAY DIFFRACTION100
3.0854-3.27860.2011550.19682653X-RAY DIFFRACTION100
3.2786-3.53160.20411270.18842673X-RAY DIFFRACTION100
3.5316-3.88660.22171380.17542671X-RAY DIFFRACTION100
3.8866-4.44810.19471260.16542716X-RAY DIFFRACTION100
4.4481-5.60070.1871340.16122724X-RAY DIFFRACTION100
5.6007-35.8450.20251560.19152795X-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