[English] 日本語
Yorodumi
- PDB-5wgb: Crystal Structure of the Human mitochondrial Cysteine Desulfurase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wgb
TitleCrystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and E. coli ACP1 protein at 2.75A
Components
  • Acyl carrier protein
  • Cysteine desulfurase, mitochondrial
  • LYR motif-containing protein 4
KeywordsTRANSFERASE / Human mitochondrial cysteine desulfurse LYR Motif containing protein 4 Acyl Carrier Protein 1 (E.coli)
Function / homology
Function and homology information


molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process ...molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / [4Fe-4S] cluster assembly / iron incorporation into metallo-sulfur cluster / L-cysteine desulfurase complex / Mitochondrial iron-sulfur cluster biogenesis / mitochondrial iron-sulfur cluster assembly complex / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / acyl carrier activity / iron-sulfur cluster binding / pyridoxal phosphate binding / nuclear body / mitochondrial matrix / centrosome / protein homodimerization activity / mitochondrion / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
LYRM4, LYR domain / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) ...LYRM4, LYR domain / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q1 / PYRIDOXAL-5'-PHOSPHATE / Acyl carrier protein / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBoniecki, M.T. / Cygler, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.
Authors: Boniecki, M.T. / Freibert, S.A. / Muhlenhoff, U. / Lill, R. / Cygler, M.
History
DepositionJul 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Refinement description / Source and taxonomy
Category: citation / entity_src_gen / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Oct 4, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase, mitochondrial
B: LYR motif-containing protein 4
C: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4615
Polymers66,6733
Non-polymers7882
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-16 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.841, 140.841, 203.301
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Cysteine desulfurase, mitochondrial /


Mass: 47395.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein LYR motif-containing protein 4


Mass: 10763.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYRM4, C6orf149, ISD11, CGI-203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD34
#3: Protein Acyl carrier protein / / ACP


Mass: 8514.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: acpP, ECS88_1108 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MJ81
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 0.3 M Ammonium Acetate 20 mM Calcium Acetate 20 mM CaCl2 19 % isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9875 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.75→32.1 Å / Num. obs: 20346 / % possible obs: 99.59 % / Redundancy: 10.9 % / CC1/2: 0.998 / Net I/σ(I): 20.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 11.3 % / Num. unique obs: 2020 / CC1/2: 0.788 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LVM

3lvm


Resolution: 2.75→32.1 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1805 8.87 %
Rwork0.2127 --
obs0.2164 20346 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 49 0 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043292
X-RAY DIFFRACTIONf_angle_d0.6774470
X-RAY DIFFRACTIONf_dihedral_angle_d5.7431994
X-RAY DIFFRACTIONf_chiral_restr0.047534
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.82440.33341370.28441415X-RAY DIFFRACTION100
2.8244-2.90740.33491370.26331403X-RAY DIFFRACTION100
2.9074-3.00120.33191380.24561416X-RAY DIFFRACTION100
3.0012-3.10840.3581390.27681426X-RAY DIFFRACTION100
3.1084-3.23280.32951360.25671402X-RAY DIFFRACTION100
3.2328-3.37980.29781390.24881428X-RAY DIFFRACTION100
3.3798-3.55780.32761380.24221405X-RAY DIFFRACTION100
3.5578-3.78050.27141400.22841441X-RAY DIFFRACTION100
3.7805-4.0720.26611380.20351423X-RAY DIFFRACTION100
4.072-4.4810.23271390.18531423X-RAY DIFFRACTION100
4.481-5.12770.24391390.18771442X-RAY DIFFRACTION100
5.1277-6.45360.23681430.21871452X-RAY DIFFRACTION100
6.4536-34.86680.21031420.19581465X-RAY DIFFRACTION97
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)
11.9850.66240.30193.1322-0.81271.54370.15680.0830.0093-0.13310.0070.34070.3846-0.1932-0.15270.7324-0.1184-0.07120.5985-0.01550.4335-19.545858.3965221.4456
25.1480.34212.79833.33281.01885.74040.61550.1758-0.27210.0112-0.67370.14080.7777-0.01190.08041.402-0.34-0.26040.88760.12990.8215-35.552232.1019219.0884
37.53424.197-2.08895.8201-0.04075.36620.31360.60950.00580.1495-0.03031.07360.7307-1.59260.03861.2411-0.3346-0.15961.33730.19911.503-55.338128.6925214.3707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 65:431 OR RESID 501:501 ) )A65 - 431
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 65:431 OR RESID 501:501 ) )A501
3X-RAY DIFFRACTION2( CHAIN B AND RESID 3:77 )B3 - 77
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:73 OR RESID 301:301 ) )C3 - 73
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 3:73 OR RESID 301:301 ) )C301

+
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