[English] 日本語
Yorodumi
- PDB-6n1o: Oxidized rat cytochrome c mutant (S47E) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n1o
TitleOxidized rat cytochrome c mutant (S47E)
ComponentsCytochrome c, somatic
KeywordsOXIDOREDUCTASE / oxidative phosphorylation / cytochrome / phosphomimetic / stability
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 / apoptosome / positive regulation of cellular respiration / Regulation of the apoptosome activity / negative regulation of hydrogen peroxide biosynthetic process / response to gravity / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / hydrogen peroxide metabolic process / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to ischemia / mitochondrial intermembrane space / response to oxidative stress / electron transfer activity / apoptotic process / heme binding / enzyme binding / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEXACYANOFERRATE(3-) / HEME C / Cytochrome c, somatic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsHuttemann, M. / Edwards, B.F.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM1166807 United States
CitationJournal: Faseb J. / Year: 2019
Title: Serine-47 phosphorylation of cytochromecin the mammalian brain regulates cytochromecoxidase and caspase-3 activity.
Authors: Kalpage, H.A. / Vaishnav, A. / Liu, J. / Varughese, A. / Wan, J. / Turner, A.A. / Ji, Q. / Zurek, M.P. / Kapralov, A.A. / Kagan, V.E. / Brunzelle, J.S. / Recanati, M.A. / Grossman, L.I. / ...Authors: Kalpage, H.A. / Vaishnav, A. / Liu, J. / Varughese, A. / Wan, J. / Turner, A.A. / Ji, Q. / Zurek, M.P. / Kapralov, A.A. / Kagan, V.E. / Brunzelle, J.S. / Recanati, M.A. / Grossman, L.I. / Sanderson, T.H. / Lee, I. / Salomon, A.R. / Edwards, B.F.P. / Huttemann, M.
History
DepositionNov 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c, somatic
B: Cytochrome c, somatic
C: Cytochrome c, somatic
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,60314
Polymers46,1574
Non-polymers3,44610
Water6,251347
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4945
Polymers11,5391
Non-polymers9554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5824
Polymers11,5391
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3703
Polymers11,5391
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3703
Polymers11,5391
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1582
Polymers11,5391
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.705, 52.357, 61.819
Angle α, β, γ (deg.)109.890, 92.660, 91.150
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 104 / Label seq-ID: 1 - 104

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Cytochrome c, somatic


Mass: 11539.329 Da / Num. of mol.: 4 / Mutation: S48E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cycs / Production host: Escherichia coli (E. coli) / References: UniProt: P62898
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6FeN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.15 % / Description: 0.1mm x 0.1 mm hexagons
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: JBS7D5: 47% MPD, 2% tert Butanol / PH range: 5.5-6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 27, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→58.04 Å / Num. obs: 56969 / % possible obs: 96.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.048 / Rrim(I) all: 0.074 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.72.10.296134360.8620.2630.39894.9
3.8-58.042.20.03739230.9950.0320.04997.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.11 Å49.2 Å
Translation2.11 Å49.2 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c0z.pdb

5c0z


Resolution: 1.55→58.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.056 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 2880 5.1 %RANDOM
Rwork0.1661 ---
obs0.1675 54088 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.95 Å2 / Biso mean: 24.392 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-1.74 Å2-0.42 Å2
2--0.22 Å2-0.46 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.55→58.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 232 347 3819
Biso mean--16.19 33.21 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183326
X-RAY DIFFRACTIONr_angle_refined_deg2.3441.7874840
X-RAY DIFFRACTIONr_angle_other_deg1.4411.6527762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28924.444144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.193158
X-RAY DIFFRACTIONr_chiral_restr0.1320.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02684
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A32250.07
12B32250.07
21A31990.09
22C31990.09
31A31860.08
32D31860.08
41B32330.08
42C32330.08
51B32300.07
52D32300.07
61C32510.07
62D32510.07
LS refinement shellResolution: 1.552→1.593 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 231 -
Rwork0.279 3929 -
all-4160 -
obs--94.33 %
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)
12.18180.72380.10722.59390.23032.68350.0238-0.05160.0040.0914-0.0585-0.022-0.07130.0130.03460.01660.01740.00860.04090.02750.03619.90215.2357.577
22.22040.1426-0.32473.0083-0.50673.0264-0.10360.11780.0202-0.15250.07380.03990.0855-0.11330.02970.01730.00080.00580.0390.02640.033.6951.116-20.199
32.19680.68530.0773.33730.20872.1979-0.01530.0424-0.1144-0.06450.0144-0.15080.1567-0.0690.00090.03530.01030.00270.04050.03330.0622-4.999-17.768-5.047
42.39810.55710.23272.04570.05193.01810.0448-0.11290.01720.09-0.02430.0097-0.0305-0.0344-0.02050.02690.0020.0050.05030.04150.04929.896-3.43922.197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2B1 - 104
3X-RAY DIFFRACTION3C1 - 104
4X-RAY DIFFRACTION4D1 - 104

+
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