[English] 日本語
Yorodumi
- PDB-8uc5: Apo X-ray crystal structure of Cyclophilin D with a surface entro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uc5
TitleApo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / Peptidyl prolyl isomerase / Cyclophilin D / mitochondria
Function / homology
Function and homology information


regulation of proton-transporting ATPase activity, rotational mechanism / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / mitochondrial depolarization / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / apoptotic mitochondrial changes / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / peptide binding / cellular response to calcium ion / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsKreitler, D.F. / Rangwala, A.M. / Seeliger, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119437 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30CA260771 United States
CitationJournal: To Be Published
Title: Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I)
Authors: Kreitler, D.F. / Seeliger, M.A. / Rangwala, A.M.
History
DepositionSep 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
B: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,61419
Polymers53,6023
Non-polymers1,01216
Water6,287349
1
X: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,43010
Polymers17,8671
Non-polymers5639
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1606
Polymers17,8671
Non-polymers2935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0243
Polymers17,8671
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.667, 56.643, 101.172
Angle α, β, γ (deg.)90.000, 123.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CyP-D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17867.334 Da / Num. of mol.: 3 / Mutation: K175I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 % / Description: 3D
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Well solution: 2.1 M DL-Malic acid pH 7.0. Protein solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol. Drop: 1 uL protein, 1 uL well solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2022 / Details: KB
RadiationMonochromator: DCM Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.43→29.33 Å / Num. obs: 105128 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.24 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.093 / Net I/σ(I): 8.8
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7331 / CC1/2: 0.657 / Rrim(I) all: 0.807 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
DIMPLEphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→29.33 Å / SU ML: 0.1273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7574
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1754 1996 1.9 %
Rwork0.1442 103124 -
obs0.1448 105120 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.71 Å2
Refinement stepCycle: LAST / Resolution: 1.43→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 49 349 4139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013916
X-RAY DIFFRACTIONf_angle_d1.12245285
X-RAY DIFFRACTIONf_chiral_restr0.095576
X-RAY DIFFRACTIONf_plane_restr0.0058687
X-RAY DIFFRACTIONf_dihedral_angle_d11.51281414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.460.2571310.21117001X-RAY DIFFRACTION92.89
1.46-1.50.24191440.19087292X-RAY DIFFRACTION96.75
1.5-1.550.23251470.17417260X-RAY DIFFRACTION96.84
1.55-1.60.2461340.16367291X-RAY DIFFRACTION97.07
1.6-1.660.19121390.15137343X-RAY DIFFRACTION97.32
1.66-1.720.1891350.13827357X-RAY DIFFRACTION97.49
1.72-1.80.19471480.12987342X-RAY DIFFRACTION97.69
1.8-1.890.15441440.12367418X-RAY DIFFRACTION98.03
1.89-2.010.15651390.12167368X-RAY DIFFRACTION97.98
2.01-2.170.15651530.1217402X-RAY DIFFRACTION98.05
2.17-2.390.18191360.13037427X-RAY DIFFRACTION98.25
2.39-2.730.181440.15517412X-RAY DIFFRACTION97.62
2.73-3.440.19661470.14887508X-RAY DIFFRACTION98.56
3.44-29.330.14151550.14727703X-RAY DIFFRACTION99.3

+
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