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- PDB-2ypt: Crystal structure of the human nuclear membrane zinc metalloprote... -

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Basic information

Entry
Database: PDB / ID: 2ypt
TitleCrystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A
Components
  • CAAX PRENYL PROTEASE 1 HOMOLOG
  • PRELAMIN-A/C
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / 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 / negative regulation of mesenchymal cell proliferation / structural constituent of nuclear lamina / ventricular cardiac muscle cell development / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / cardiac ventricle development / nuclear envelope organization / growth plate cartilage development / maintenance of rDNA / regulation of fibroblast proliferation / nuclear pore localization / Nuclear Envelope Breakdown / calcium ion import into sarcoplasmic reticulum / regulation of cellular senescence / ventricular cardiac muscle tissue development / lamin filament / protein localization to nuclear envelope / CAMKK-AMPK signaling cascade / cardiac conduction / regulation of TOR signaling / XBP1(S) activates chaperone genes / regulation of defense response to virus / positive regulation of gene expression via chromosomal CpG island demethylation / nuclear lamina / metalloexopeptidase activity / regulation of bone mineralization / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of miRNA processing / nuclear inner membrane / cardiac muscle cell development / regulation of telomere maintenance / adult walking behavior / intermediate filament / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cardiac muscle hypertrophy in response to stress / nuclear migration / neuromuscular process / muscle organ development / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / bone mineralization / negative regulation of release of cytochrome c from mitochondria / regulation of lipid metabolic process / regulation of glucose metabolic process / regulation of multicellular organism growth / hair follicle development / protein localization to nucleus / heart morphogenesis / Meiotic synapsis / protein maturation / regulation of cell migration / liver development / thymus development / negative regulation of extrinsic apoptotic signaling pathway / determination of adult lifespan / cellular response to gamma radiation / regulation of protein stability / multicellular organism growth / metalloendopeptidase activity / structural constituent of cytoskeleton / lipid metabolic process / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome membrane / intracellular protein localization / nuclear envelope / heterochromatin formation / regulation of cell shape / site of double-strand break / double-stranded DNA binding / early endosome membrane / endopeptidase activity / cellular response to hypoxia / nuclear membrane / regulation of autophagy / nuclear speck / negative regulation of cell population proliferation / DNA repair / positive regulation of gene expression / endoplasmic reticulum membrane / perinuclear region of cytoplasm / structural molecule activity / protein-containing complex / proteolysis / extracellular exosome
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 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. ...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 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Zincin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CAAX prenyl protease 1 homolog / Prelamin-A/C
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.8 Å
AuthorsPike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Savitsky, P. / Cooper, C.D.O. / Chaikuad, A. / Goubin, S. / Shrestha, L. / Li, Q. ...Pike, A.C.W. / Dong, Y.Y. / Quigley, A. / Dong, L. / Savitsky, P. / 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
DepositionNov 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_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

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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
F: PRELAMIN-A/C
G: PRELAMIN-A/C
H: PRELAMIN-A/C
I: PRELAMIN-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,66612
Polymers224,4048
Non-polymers2624
Water00
1
D: CAAX PRENYL PROTEASE 1 HOMOLOG
H: PRELAMIN-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1663
Polymers56,1012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-47.7 kcal/mol
Surface area22130 Å2
MethodPISA
2
A: CAAX PRENYL PROTEASE 1 HOMOLOG
F: PRELAMIN-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1663
Polymers56,1012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-45.9 kcal/mol
Surface area22450 Å2
MethodPISA
3
B: CAAX PRENYL PROTEASE 1 HOMOLOG
G: PRELAMIN-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1663
Polymers56,1012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-46.8 kcal/mol
Surface area22100 Å2
MethodPISA
4
E: CAAX PRENYL PROTEASE 1 HOMOLOG
I: PRELAMIN-A/C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1663
Polymers56,1012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-46.2 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 95.540, 132.030
Angle α, β, γ (deg.)76.26, 79.67, 72.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99996, -0.00494, -0.00677), (-0.00417, -0.40661, 0.91359), (-0.00727, 0.91359, 0.40658)297.16388, 88.52379, -55.95213
2given(-0.99975, -0.00638, 0.02154), (-0.02236, 0.37909, -0.92509), (-0.00226, -0.92534, -0.37913)300.23688, 243.94095, 398.61621
3given(0.99998, -0.00139, -0.00596), (-0.00127, -0.99982, 0.01868), (-0.00599, -0.01867, -0.99981)-5.96792, 355.48517, 323.57315

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Components

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


Mass: 55648.473 Da / Num. of mol.: 4 / Mutation: YES
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: Protein/peptide
PRELAMIN-A/C / 70 KDA LAMIN / RENAL CARCINOMA ANTIGEN NY-REN-32 / PRELAMIN A


Mass: 452.589 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02545
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Sequence detailsCATALYTIC MUTANT. PUTATIVE CATALYTIC RESIDUE GLU336 MUTATED TO ALANINE

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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: 3.2 Å3/Da / Density % sol: 61.55 % / Description: NONE
Crystal growpH: 7
Details: 0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(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: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.8→38.5 Å / Num. obs: 26943 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 134.21 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.8→38.5 Å / Cor.coef. Fo:Fc: 0.8843 / Cor.coef. Fo:Fc free: 0.8837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.687
Details: 4AW6 USED AS LSSR TARGET REST OF 0.1. AUTONCS AND TLS. ONE TLS GROUP PER ENZYME PEPTIDE COMPLEX EMPLOYED
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 1420 5.27 %RANDOM
Rwork0.2625 ---
obs0.2635 26939 99.33 %-
Displacement parametersBiso mean: 173.48 Å2
Baniso -1Baniso -2Baniso -3
1--10.3701 Å2-5.7593 Å2-8.3756 Å2
2--12.8077 Å2-3.6883 Å2
3----2.4377 Å2
Refine analyzeLuzzati coordinate error obs: 1.324 Å
Refinement stepCycle: LAST / Resolution: 3.8→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12481 0 4 0 12485
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812864HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8617608HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5406SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1966HARMONIC5
X-RAY DIFFRACTIONt_it12864HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.73
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1757SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14868SEMIHARMONIC4
LS refinement shellResolution: 3.8→3.94 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2487 147 5.22 %
Rwork0.2242 2668 -
all0.2256 2815 -
obs--99.33 %
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)
12.68690.168-1.25682.8313-2.10166.55910.30490.48130.45720.0703-0.1990.0085-1.5283-0.5475-0.1059-0.05220.2883-0.0698-0.1621-0.0353-0.3706146.3041204.0154179.1445
23.2546-0.007-0.59945.6486-0.9422.86690.1822-0.1805-0.98050.9779-0.1532-0.39050.89220.094-0.029-0.0789-0.0241-0.2943-0.388-0.0975-0.0111147.9806168.4296201.8755
33.6029-1.0246-0.52738.9250.31033.1699-0.11790.07580.2962-1.62280.2265-0.7881-0.64190.1031-0.1087-0.1323-0.10580.2228-0.3263-0.0215-0.3283154.477189.2683117.1085
44.301-1.0202-0.56572.9711-1.04935.4759-0.8008-0.9853-1.21960.49760.41150.26471.688-0.15770.38930.0480.16010.3565-0.34220.3185-0.1281154.2415154.122141.1313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - A|600 F|661 - F|663 }
2X-RAY DIFFRACTION2{B|10 - B|600 G|661 - G|664 }
3X-RAY DIFFRACTION3{D|10 - D|600 H|661 - H|664 }
4X-RAY DIFFRACTION4{E|10 - E|600 I|661 - I|663 }

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