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- PDB-6ecj: Human cytochrome c G41T -

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Basic information

Entry
Database: PDB / ID: 6ecj
TitleHuman cytochrome c G41T
ComponentsCytochrome c
KeywordsAPOPTOSIS / cytochrome c / heme / glycine to threonine substitution
Function / homology
Function and homology information


Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / Pyroptosis / respirasome / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / nucleus / 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
HEME C / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
Model detailsG41T variant
AuthorsFellner, M. / Jameson, G.N.L. / Ledgerwood, E.C. / Wilbanks, S.M.
CitationJournal: Biochem.J. / Year: 2021
Title: Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity.
Authors: Fellner, M. / Parakra, R. / McDonald, K.O. / Kass, I. / Jameson, G.N.L. / Wilbanks, S.M. / Ledgerwood, E.C.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 2.0Feb 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _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_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c
B: Cytochrome c
C: Cytochrome c
D: Cytochrome c
E: Cytochrome c
F: Cytochrome c
G: Cytochrome c
H: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,42516
Polymers93,4778
Non-polymers4,9488
Water3,351186
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3032
Polymers11,6851
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.060, 76.170, 232.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 or (resid 2 through 5...
21(chain B and (resid 1 or (resid 2 through 5...
31(chain C and (resid 1 or (resid 2 through 5...
41(chain D and (resid 1 or (resid 2 through 5...
51(chain E and (resid 1 or (resid 2 through 5...
61(chain F and (resid 1 or (resid 2 through 5...
71(chain G and (resid 1 or (resid 2 through 5...
81(chain H and (resid 1 through 52 or (resid 53...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 or (resid 2 through 5...A1
121(chain A and (resid 1 or (resid 2 through 5...A2 - 5
131(chain A and (resid 1 or (resid 2 through 5...A1 - 105
141(chain A and (resid 1 or (resid 2 through 5...A1 - 105
151(chain A and (resid 1 or (resid 2 through 5...A1 - 105
161(chain A and (resid 1 or (resid 2 through 5...A1 - 105
211(chain B and (resid 1 or (resid 2 through 5...B1
221(chain B and (resid 1 or (resid 2 through 5...B2 - 5
231(chain B and (resid 1 or (resid 2 through 5...B1 - 105
241(chain B and (resid 1 or (resid 2 through 5...B1 - 105
251(chain B and (resid 1 or (resid 2 through 5...B1 - 105
261(chain B and (resid 1 or (resid 2 through 5...B1 - 105
311(chain C and (resid 1 or (resid 2 through 5...C1
321(chain C and (resid 1 or (resid 2 through 5...C2 - 5
331(chain C and (resid 1 or (resid 2 through 5...C1 - 105
341(chain C and (resid 1 or (resid 2 through 5...C1 - 105
351(chain C and (resid 1 or (resid 2 through 5...C1 - 105
361(chain C and (resid 1 or (resid 2 through 5...C1 - 105
411(chain D and (resid 1 or (resid 2 through 5...D1
421(chain D and (resid 1 or (resid 2 through 5...D2 - 5
431(chain D and (resid 1 or (resid 2 through 5...D1 - 105
441(chain D and (resid 1 or (resid 2 through 5...D1 - 105
451(chain D and (resid 1 or (resid 2 through 5...D1 - 105
511(chain E and (resid 1 or (resid 2 through 5...E1
521(chain E and (resid 1 or (resid 2 through 5...E2 - 5
531(chain E and (resid 1 or (resid 2 through 5...E1 - 105
541(chain E and (resid 1 or (resid 2 through 5...E1 - 105
551(chain E and (resid 1 or (resid 2 through 5...E1 - 105
611(chain F and (resid 1 or (resid 2 through 5...F1
621(chain F and (resid 1 or (resid 2 through 5...F2 - 5
631(chain F and (resid 1 or (resid 2 through 5...F1 - 105
641(chain F and (resid 1 or (resid 2 through 5...F1 - 105
651(chain F and (resid 1 or (resid 2 through 5...F1 - 105
661(chain F and (resid 1 or (resid 2 through 5...F1 - 105
711(chain G and (resid 1 or (resid 2 through 5...G1
721(chain G and (resid 1 or (resid 2 through 5...G2 - 5
731(chain G and (resid 1 or (resid 2 through 5...G1 - 105
741(chain G and (resid 1 or (resid 2 through 5...G1 - 105
751(chain G and (resid 1 or (resid 2 through 5...G1 - 105
761(chain G and (resid 1 or (resid 2 through 5...G1 - 105
811(chain H and (resid 1 through 52 or (resid 53...H1 - 52
821(chain H and (resid 1 through 52 or (resid 53...H53
831(chain H and (resid 1 through 52 or (resid 53...H1 - 105
841(chain H and (resid 1 through 52 or (resid 53...H1 - 105
851(chain H and (resid 1 through 52 or (resid 53...H1 - 105
861(chain H and (resid 1 through 52 or (resid 53...H1 - 105
871(chain H and (resid 1 through 52 or (resid 53...H1 - 105
881(chain H and (resid 1 through 52 or (resid 53...H1 - 105

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Components

#1: Protein
Cytochrome c /


Mass: 11684.635 Da / Num. of mol.: 8 / Mutation: G41T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC / Plasmid: pBTR(HumanCc) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P99999
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.14 % / Mosaicity: 0.41 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hanging drops of 1 microL of 30.1 mg/mL of reduced protein and 1 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (30% (w/v) polyethylene glycol 5000, 60 mM ...Details: Hanging drops of 1 microL of 30.1 mg/mL of reduced protein and 1 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (30% (w/v) polyethylene glycol 5000, 60 mM lithiumsulfate, 50 mM Tris-HCl pH 8.5). The protein solution was 26 mM sodium phosphate, 37 mM sodium chloride, 14 mM sodium dithionite (pH 7.6).

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→77.61 Å / Num. obs: 32753 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.085 / Rrim(I) all: 0.229 / Net I/σ(I): 7.9 / Num. measured all: 233952 / Scaling rejects: 171
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.764 / Num. unique obs: 4277 / CC1/2: 0.852 / Rpim(I) all: 0.303 / Rrim(I) all: 0.823 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.2 Å72.39 Å
Translation8.2 Å72.39 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASER2.6.0phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NWV

3nwv


Resolution: 2.7→65.06 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2486 1598 4.92 %
Rwork0.2149 --
obs0.2166 32683 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.06 Å2 / Biso mean: 27.7552 Å2 / Biso min: 5.68 Å2
Refinement stepCycle: final / Resolution: 2.7→65.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 344 186 6741
Biso mean--21.05 22.78 -
Num. residues----832
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2544X-RAY DIFFRACTION6.643TORSIONAL
12B2544X-RAY DIFFRACTION6.643TORSIONAL
13C2544X-RAY DIFFRACTION6.643TORSIONAL
14D2544X-RAY DIFFRACTION6.643TORSIONAL
15E2544X-RAY DIFFRACTION6.643TORSIONAL
16F2544X-RAY DIFFRACTION6.643TORSIONAL
17G2544X-RAY DIFFRACTION6.643TORSIONAL
18H2544X-RAY DIFFRACTION6.643TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.74220.35341410.294526332774
2.7422-2.78710.26961180.279926852803
2.7871-2.83520.33561410.270126522793
2.8352-2.88680.30831130.256126322745
2.8868-2.94230.28251370.25326802817
2.9423-3.00230.28421400.251426092749
3.0023-3.06760.321160.264427182834
3.0676-3.1390.31431580.275226492807
3.139-3.21750.28921370.246726222759
3.2175-3.30450.27141420.245826542796
3.3045-3.40170.29181190.217826652784
3.4017-3.51150.27191290.21326502779
3.5115-3.6370.23981530.216226642817
3.637-3.78260.23211050.214326712776
3.7826-3.95470.22461480.193226352783
3.9547-4.16320.28061520.187126512803
4.1632-4.4240.16651400.1626302770
4.424-4.76550.21661760.1726512827
4.7655-5.24480.18331320.17726402772
5.2448-6.00330.20431460.179526422788
6.0033-7.56170.21281550.192326332788
7.5617-65.07880.20991200.197426642784

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