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- PDB-4aw6: Crystal structure of the human nuclear membrane zinc metalloprote... -

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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 / positive regulation of gene expression via chromosomal CpG island demethylation / inflammatory cell apoptotic process / regulation of hormone metabolic process / 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 / positive regulation of gene expression via chromosomal CpG island demethylation / inflammatory cell apoptotic process / regulation of hormone metabolic process / response to DNA damage checkpoint signaling / kidney morphogenesis / cellular lipid metabolic process / cardiac ventricle development / maintenance of rDNA / nuclear envelope organization / growth plate cartilage development / ventricular cardiac muscle tissue development / regulation of fibroblast proliferation / calcium ion import into sarcoplasmic reticulum / regulation of cellular senescence / regulation of TOR signaling / CAMKK-AMPK signaling cascade / cardiac conduction / regulation of defense response to virus / metalloexopeptidase activity / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / adult walking behavior / : / negative regulation of miRNA processing / cardiac muscle cell development / nuclear inner membrane / regulation of DNA damage response, signal transduction by p53 class mediator / neuromuscular process / bone mineralization / regulation of lipid metabolic process / regulation of multicellular organism growth / regulation of glucose metabolic process / hair follicle development / heart morphogenesis / thymus development / liver development / regulation of autophagy / determination of adult lifespan / multicellular organism growth / cellular response to gamma radiation / metalloendopeptidase activity / late endosome membrane / regulation of cell shape / double-stranded DNA binding / early endosome membrane / DNA repair / endoplasmic reticulum membrane / protein-containing complex / proteolysis / extracellular exosome / membrane / metal ion binding
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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.

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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 / Phosphatidylcholine


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

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Experimental details

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Experiment

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

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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

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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

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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

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