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- PDB-5exq: Human cytochrome c Y48H -

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Basic information

Entry
Database: PDB / ID: 5exq
TitleHuman cytochrome c Y48H
ComponentsCytochrome c
KeywordsAPOPTOSIS / cytochrome c / heme / tyrosine to histidine substitution / ELECTRON TRANSPORT
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-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Model detailsY48H 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
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 2.0Feb 3, 2021Group: Atomic model / Data collection ...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 / diffrn_radiation_wavelength / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _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 / _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 2.1Sep 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5645
Polymers23,2312
Non-polymers1,3333
Water6,630368
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2342
Polymers11,6161
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3303
Polymers11,6161
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.791, 35.965, 59.937
Angle α, β, γ (deg.)90.000, 115.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c /


Mass: 11615.556 Da / Num. of mol.: 2 / Mutation: Y48H
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.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hanging drops of 1 microL of 29.5 mg/mL of reduced protein and 2 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (32% (w/v) polyethylene glycol 5000, 50 mM ...Details: Hanging drops of 1 microL of 29.5 mg/mL of reduced protein and 2 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (32% (w/v) polyethylene glycol 5000, 50 mM lithiumsulfate, 50 mM Tris-HCl pH 8.5). The protein solution was 17.5 mM sodium phosphate, 25 mM sodium chloride, 15 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: 1.6→54.04 Å / Num. obs: 26388 / % possible obs: 90.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.63 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.052 / Net I/σ(I): 10.4 / Num. measured all: 97684 / Scaling rejects: 63
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.622.60.4252.6352313640.6780.32290.6
8.6-54.045.10.06522.39791930.9920.0392.5

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Processing

Software
NameVersionClassification
MOSFLM7.1.1data reduction
PHASER2.6.0phasing
PHENIX1.10-2155refinement
PDB_EXTRACT3.15data extraction
Aimless0.3.11data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZCF
Resolution: 1.6→54.038 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 2536 5.15 %
Rwork0.1726 46667 -
obs0.1737 26362 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.16 Å2 / Biso mean: 21.5129 Å2 / Biso min: 5.9 Å2
Refinement stepCycle: final / Resolution: 1.6→54.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 91 370 2089
Biso mean--12.03 33.26 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111808
X-RAY DIFFRACTIONf_angle_d0.952439
X-RAY DIFFRACTIONf_chiral_restr0.052235
X-RAY DIFFRACTIONf_plane_restr0.01301
X-RAY DIFFRACTIONf_dihedral_angle_d16.934686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5964-1.62710.29841610.24722616277787
1.6271-1.66030.25941190.24222781290094
1.6603-1.69640.30421450.23182827297293
1.6964-1.73590.22851540.21712759291393
1.7359-1.77930.24721400.20942788292893
1.7793-1.82740.23071460.20112814296093
1.8274-1.88120.26681580.19572740289892
1.8812-1.94190.2868320.272783686877
1.9419-2.01130.23541180.18032478259688
2.0113-2.09190.21531200.18212788290891
2.0919-2.18710.16341340.16532704283890
2.1871-2.30240.2105570.195491797431
2.3024-2.44660.17841560.166129743130100
2.4466-2.63550.1742070.1632921312899
2.6355-2.90070.16341590.16212974313399
2.9007-3.32040.19161870.16542961314899
3.3204-4.18320.16972430.14492842308598
4.1832-54.06940.14821000.1442947304797
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.58341.68120.11665.36150.38044.22320.054-1.13730.17260.3175-0.091-0.1653-0.14760.22030.03450.13890.0188-0.02490.2701-0.00660.0944-2.2507-1.3552-6.5092
25.57551.05462.69592.00280.12844.60860.0311-0.0193-0.54110.05020.0482-0.18130.43480.1945-0.09840.1250.02050.01240.0858-0.0040.1566-1.1497-12.5999-17.8794
37.30060.80034.52796.005-0.30449.15020.12380.33810.3822-0.16580.0918-0.4408-0.21490.2701-0.20520.0883-0.00990.0450.091-0.02040.1282-0.578-0.757-22.7661
45.62690.80050.85340.97861.72986.0272-0.04030.09380.4949-0.01170.16670.0162-0.15120.0227-0.09780.0493-0.00060.00460.07870.0210.1143-8.2356-0.1827-19.9444
58.6471-0.12671.15817.2745-3.70689.42440.0974-0.47790.63460.163-0.0306-0.2447-0.34860.9292-0.03850.0893-0.04110.02450.2306-0.11060.21545.14992.2384-11.7524
69.4347-0.92962.21346.75033.77372.1250.2168-0.36350.42970.0533-0.1201-0.0036-0.9753-0.646-0.07380.18690.03610.00090.12470.00470.1422-35.339315.6051-10.3101
78.9994-0.5549-0.3086.25464.19555.3180.0431-0.138-0.2293-0.1596-0.1750.36980.085-0.37880.06580.0415-0.001-0.02740.123-0.02020.1046-37.00184.1406-15.4404
83.48682.4633-0.46733.86481.12077.81650.0146-0.1639-0.05640.1802-0.06930.14260.4353-0.35710.01770.1034-0.02140.01890.07710.01560.1036-31.445-1.917-12.9745
94.5081-0.0711-0.56861.46351.58634.6461-0.10780.0261-0.4075-0.03120.03910.16150.2829-0.16850.0510.1017-0.0109-0.00590.07580.00540.1291-25.4306-6.1086-18.8112
104.771-1.4746-0.49629.77-1.22018.0658-0.1109-0.4630.09180.47370.171-0.0517-0.13720.0005-0.04110.05810.0086-0.00370.130.00130.0685-20.81684.952-9.3742
115.9277-0.60951.50855.61.55796.44010.0499-0.06140.1763-0.00010.0308-0.2-0.24820.1579-0.08150.0606-0.01040.02780.07770.00940.0662-21.05968.2395-19.0438
127.96634.2897-1.27758.431-0.73859.08070.139-0.38290.1930.3703-0.0970.1425-0.2728-0.3204-0.03920.09490.04040.01190.1179-0.02840.067-31.359110.2097-5.7175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 74 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 87 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 104 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 23 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 43 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 54 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 69 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 70 through 87 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 104 )B0

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