[English] 日本語
Yorodumi
- PDB-4aw6: Crystal structure of the human nuclear membrane zinc metalloprote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aw6
TitleCrystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1)
ComponentsCAAX PRENYL PROTEASE 1 HOMOLOG
KeywordsHYDROLASE / M48 PEPTIDASE / INTEGRAL MEMBRANE PROTEIN / PRELAMIN A PROCESSING / AGEING / PROGERIA
Function / homology
Function and homology information


prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / inflammatory cell apoptotic process / regulation of hormone metabolic process / kidney morphogenesis / response to DNA damage checkpoint signaling ...prenylated protein catabolic process / regulation of stress-activated protein kinase signaling cascade / regulation of mitotic cell cycle DNA replication / regulation of termination of RNA polymerase I transcription / Ste24 endopeptidase / CAAX-box protein processing / inflammatory cell apoptotic process / regulation of hormone metabolic process / kidney morphogenesis / response to DNA damage checkpoint signaling / cardiac ventricle development / nuclear envelope organization / growth plate cartilage development / maintenance of rDNA / regulation of fibroblast proliferation / calcium ion import into sarcoplasmic reticulum / regulation of cellular senescence / ventricular cardiac muscle tissue development / CAMKK-AMPK signaling cascade / cardiac conduction / regulation of TOR signaling / regulation of defense response to virus / positive regulation of gene expression via chromosomal CpG island demethylation / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of miRNA processing / nuclear inner membrane / cardiac muscle cell development / adult walking behavior / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / bone mineralization / regulation of lipid metabolic process / regulation of glucose metabolic process / regulation of multicellular organism growth / hair follicle development / heart morphogenesis / protein maturation / liver development / thymus development / determination of adult lifespan / cellular response to gamma radiation / multicellular organism growth / metalloendopeptidase activity / lipid metabolic process / late endosome membrane / regulation of cell shape / double-stranded DNA binding / early endosome membrane / endopeptidase activity / regulation of autophagy / DNA repair / endoplasmic reticulum membrane / protein-containing complex / proteolysis / extracellular exosome / metal ion binding / membrane
Similarity search - Function
CAAX prenyl protease 1 / CAAX prenyl protease 1, N-terminal / CAAX prenyl protease N-terminal, five membrane helices / Metalloproteases ("zincins"), catalytic domain / Peptidase M48 / Peptidase family M48 / Zincin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / CAAX prenyl protease 1 homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. / Mukhopadhyay, S. ...Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. / Mukhopadhyay, S. / Yang, J. / Xia, X. / Shintre, C.A. / Barr, A.J. / Berridge, G. / Chalk, R. / Bray, J.E. / von Delft, F. / Bullock, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Burgess-Brown, N. / Carpenter, E.P.
CitationJournal: Science / Year: 2013
Title: The Structural Basis of Zmpste24-Dependent Laminopathies.
Authors: Quigley, A. / Dong, Y.Y. / Pike, A.C.W. / Dong, L. / Shrestha, L. / Berridge, G. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Burgess- ...Authors: Quigley, A. / Dong, Y.Y. / Pike, A.C.W. / Dong, L. / Shrestha, L. / Berridge, G. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Burgess-Brown, N.A. / Carpenter, E.P.
History
DepositionMay 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Structure summary
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAAX PRENYL PROTEASE 1 HOMOLOG
B: CAAX PRENYL PROTEASE 1 HOMOLOG
D: CAAX PRENYL PROTEASE 1 HOMOLOG
E: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,24812
Polymers222,8264
Non-polymers3,4228
Water00
1
A: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5623
Polymers55,7071
Non-polymers8562
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5623
Polymers55,7071
Non-polymers8562
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5623
Polymers55,7071
Non-polymers8562
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5623
Polymers55,7071
Non-polymers8562
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: CAAX PRENYL PROTEASE 1 HOMOLOG
B: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1246
Polymers111,4132
Non-polymers1,7114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-137.7 kcal/mol
Surface area41280 Å2
MethodPISA
6
D: CAAX PRENYL PROTEASE 1 HOMOLOG
E: CAAX PRENYL PROTEASE 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1246
Polymers111,4132
Non-polymers1,7114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-135.9 kcal/mol
Surface area40430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.987, 95.451, 131.095
Angle α, β, γ (deg.)76.73, 79.64, 72.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, -0.001, -0.007), (-0.006, -0.405, 0.915), (-0.003, 0.915, 0.405)296.60288, 87.8738, -56.09467
2given(-0.999, -0.016, 0.03), (-0.034, 0.38, -0.924), (0.004, -0.925, -0.381)300.97144, 245.09117, 397.95886
3given(1, 0.005, -0.008), (0.005, -1, 0.017), (-0.008, -0.017, -1)-6.6495, 354.61932, 323.63803
DetailsDETERMINED OLIGOMERIC STATE BY PISA (DIMERIC) DOES NOT MATCH OBSERVATIONS FROM IN-SOLUTION STUDIES WHERE THE PROTEIN IS MONOMERIC AS DETERMINED BY SEC/MALLS ANALYSIS. IN ADDITION THE 'DIMER' INTERFACE SEEN IN THIS ENTRY IS NOT OBSERVED IN A SECOND CRYSTAL FORM SUGGESTING THAT IT IS A FEATURE OF CRYSTAL PACKING RATHER THAN A BONA FIDE DIMERIZATION SURFACE.

-
Components

#1: Protein
CAAX PRENYL PROTEASE 1 HOMOLOG / ZMPSTE24 / FARNESYLATED PROTEINS-CONVERTING ENZYME 1 / FACE-1 / PRENYL PROTEIN-SPECIFIC ...ZMPSTE24 / FARNESYLATED PROTEINS-CONVERTING ENZYME 1 / FACE-1 / PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1 / ZINC METALLOPROTEINASE STE24 HOMOLOG


Mass: 55706.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O75844, Ste24 endopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
Sequence detailsNATURAL VARIANT THR137ALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.21 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.4→39.45 Å / Num. obs: 37469 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 129.24 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
SOLVEphasing
BUSTER-TNTBUSTER 2.11.2refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.4→37.96 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.8802 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1927 5.14 %RANDOM
Rwork0.2457 ---
obs0.2466 37465 99.97 %-
Displacement parametersBiso mean: 131.61 Å2
Baniso -1Baniso -2Baniso -3
1--23.0565 Å2-4.2512 Å2-1.749 Å2
2--11.469 Å2-6.3922 Å2
3---11.5874 Å2
Refine analyzeLuzzati coordinate error obs: 1.021 Å
Refinement stepCycle: LAST / Resolution: 3.4→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12838 0 112 0 12950
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813350HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8718213HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes195HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1994HARMONIC5
X-RAY DIFFRACTIONt_it13350HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion2.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1768SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15607SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2551 124 4.27 %
Rwork0.231 2777 -
all0.232 2901 -
obs--99.97 %
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)
12.01080.1251-0.4562.8862-1.97285.51190.17120.34870.37480.0894-0.04590.0743-1.279-0.3337-0.1253-0.13110.191-0.0088-0.16560.0377-0.406146.5373204.0057178.8764
23.0010.6-0.15525.3623-1.58743.04070.1321-0.0993-0.71390.5071-0.1433-0.34550.57910.06670.0112-0.31760.0063-0.1654-0.3968-0.0694-0.1708147.9097167.9031202.1341
32.2065-0.49190.08887.5226-0.95992.5874-0.13530.05070.1793-1.09750.1563-0.5982-0.23190.0143-0.021-0.3297-0.07150.199-0.2949-0.0563-0.2826154.2673189.7487116.9939
42.9836-0.4945-0.45152.7254-1.08754.5116-0.7084-0.6153-0.79170.37020.33810.17421.5325-0.02860.3703-0.00940.14780.2863-0.3920.2184-0.3618154.2025154.2191141.0959

+
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