[English] 日本語
Yorodumi
- PDB-3iei: Crystal structure of human leucine carboxylmethyltransferase-1 in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iei
TitleCrystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine
ComponentsLeucine carboxyl methyltransferase 1
KeywordsTRANSFERASE / LCMT-1 / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


protein C-terminal carboxyl O-methyltransferase activity / C-terminal protein methylation / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / regulation of mitotic cell cycle spindle assembly checkpoint / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / regulation of glucose metabolic process / negative regulation of protein-containing complex assembly / Cyclin A/B1/B2 associated events during G2/M transition ...protein C-terminal carboxyl O-methyltransferase activity / C-terminal protein methylation / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / regulation of mitotic cell cycle spindle assembly checkpoint / protein methylation / S-adenosylmethionine-dependent methyltransferase activity / regulation of glucose metabolic process / negative regulation of protein-containing complex assembly / Cyclin A/B1/B2 associated events during G2/M transition / protein modification process / G2/M transition of mitotic cell cycle / regulation of apoptotic process / nucleoplasm / cytosol
Similarity search - Function
Leucine carboxyl methyltransferase 1 / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXing, Y. / Jeffry, P.D.
CitationJournal: To be Published
Title: Structural Insights into Novel Functions of a pro-survival PP2A-specific Methyltransferase
Authors: Stanevich, V. / Jiang, L. / Satyshur, K.A. / Li, Y. / Jeffrey, P.D. / Li, Z. / Semmelhack, M.F. / Xing, Y.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine carboxyl methyltransferase 1
B: Leucine carboxyl methyltransferase 1
C: Leucine carboxyl methyltransferase 1
D: Leucine carboxyl methyltransferase 1
E: Leucine carboxyl methyltransferase 1
F: Leucine carboxyl methyltransferase 1
G: Leucine carboxyl methyltransferase 1
H: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,62728
Polymers308,0348
Non-polymers4,59320
Water33,3461851
1
A: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,5041
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1764
Polymers38,5041
Non-polymers6723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,5041
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1764
Polymers38,5041
Non-polymers6723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1764
Polymers38,5041
Non-polymers6723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,5041
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,5041
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Leucine carboxyl methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1764
Polymers38,5041
Non-polymers6723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.036, 81.127, 82.816
Angle α, β, γ (deg.)105.41, 93.97, 104.29
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Leucine carboxyl methyltransferase 1 / Protein-leucine O-methyltransferase


Mass: 38504.211 Da / Num. of mol.: 8 / Mutation: C19M, A21E, D22N, P115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-68, LCMT, LCMT-1, LCMT1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UIC8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1851 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR ...Details: Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2005
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationMonochromator: Double Si(111) crystal with cryogenically-cooled first crystal and sagitally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 210536 / Num. obs: 210536 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.057 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.28 / Num. unique all: 11786 / Rsym value: 0.511 / % possible all: 50

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RFG

1rfg


Resolution: 1.9→29.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.326 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23224 9650 5 %RANDOM
Rwork0.18359 ---
obs0.18601 181902 95.27 %-
all-190933 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.186 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20040 0 304 1851 22195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02220735
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.98527931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04652474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16323.77976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.641153881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.64115168
X-RAY DIFFRACTIONr_chiral_restr0.0780.23061
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115376
X-RAY DIFFRACTIONr_mcbond_it0.6141.512390
X-RAY DIFFRACTIONr_mcangle_it1.189219939
X-RAY DIFFRACTIONr_scbond_it1.6838345
X-RAY DIFFRACTIONr_scangle_it2.8244.57992
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 529 -
Rwork0.231 10204 -
obs--72.29 %

+
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