[English] 日本語
Yorodumi
- PDB-3l8i: Crystal structure of CCM3, a cerebral cavernous malformation prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l8i
TitleCrystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity
ComponentsProgrammed cell death protein 10
KeywordsPROTEIN BINDING / cerebral cavernous malformation / FAT domain / dimerization
Function / homology
Function and homology information


FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport / negative regulation of cell migration involved in sprouting angiogenesis ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / positive regulation of Notch signaling pathway / regulation of angiogenesis / cellular response to leukemia inhibitory factor / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / angiogenesis / protein stabilization / intracellular signal transduction / positive regulation of cell migration / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1950 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #70 / Programmed cell death protein 10 / Programmed cell death protein 10, C-terminal / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / Nucleotidyltransferases domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsLi, X. / Zhang, R. / Zhang, H. / He, Y. / Ji, W. / Min, W. / Boggon, T.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity.
Authors: Li, X. / Zhang, R. / Zhang, H. / He, Y. / Ji, W. / Min, W. / Boggon, T.J.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 10
B: Programmed cell death protein 10
C: Programmed cell death protein 10
D: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)99,7234
Polymers99,7234
Non-polymers00
Water1,26170
1
A: Programmed cell death protein 10
B: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)49,8622
Polymers49,8622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-40 kcal/mol
Surface area22110 Å2
MethodPISA
2
C: Programmed cell death protein 10
D: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)49,8622
Polymers49,8622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-37 kcal/mol
Surface area22810 Å2
MethodPISA
3
A: Programmed cell death protein 10
B: Programmed cell death protein 10

C: Programmed cell death protein 10
D: Programmed cell death protein 10


Theoretical massNumber of molelcules
Total (without water)99,7234
Polymers99,7234
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10750 Å2
ΔGint-89 kcal/mol
Surface area41600 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-95 kcal/mol
Surface area42240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.083, 116.008, 123.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Programmed cell death protein 10 / / TF-1 cell apoptosis-related protein 15 / Cerebral cavernous malformations 3 protein


Mass: 24930.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10, CCM3, TFAR15 / Plasmid: modified pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BUL8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M potassium fluoride, 13% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9551 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9551 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 32150 / Num. obs: 31805 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 68 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 3069 / Rsym value: 0.661

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 28.888 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28841 1600 5.1 %RANDOM
Rwork0.22932 ---
obs0.23232 30022 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.332 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2--0.64 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 0 70 6725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226756
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9719087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8085810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6225.046329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.794151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3471541
X-RAY DIFFRACTIONr_chiral_restr0.0810.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214959
X-RAY DIFFRACTIONr_mcbond_it0.4171.54082
X-RAY DIFFRACTIONr_mcangle_it0.80126640
X-RAY DIFFRACTIONr_scbond_it1.20632674
X-RAY DIFFRACTIONr_scangle_it1.9884.52447
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 101 -
Rwork0.302 2168 -
obs--97.63 %
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)
16.7908-0.2169-0.90235.26550.13587.6218-0.03560.3504-0.4168-0.0104-0.0619-0.1130.07660.48470.09750.01850.0198-0.02190.17830.02610.1713-10.14845.075-36.9522
27.45272.2548-1.81443.0884-1.44617.4281-0.26370.5965-1.0302-0.20020.0873-0.27060.60320.15360.17640.08560.06240.03090.1792-0.03050.374-22.95080.7727-38.1812
37.26610.6886-0.98675.218-1.16651.06980.1101-0.4641-0.58510.4069-0.1213-0.170.09710.00880.01120.1443-0.0377-0.09510.20040.0640.20282.80396.9987-26.9167
47.8432-1.50290.91794.61561.25269.467-0.0927-0.6755-0.51960.22920.05590.10020.215-0.57670.03680.0662-0.0211-0.02440.15530.03780.217217.9213.6926-25.9071
51.2845-0.0448-0.29840.336-0.00780.4022-0.0726-0.0177-0.08240.00540.0454-0.08570.17550.07160.02720.4940.029-0.01870.46450.00940.5394-1.9089.1716-32.1548
62.7375-2.72081.40443.5088-4.052811.68-0.1746-0.57770.09430.2780.2334-0.0322-0.16570.3936-0.05880.2183-0.0756-0.12620.3541-0.07530.1859-29.41745.7586-10.0846
75.19680.23881.86876.6401-4.49559.0788-0.08190.83810.4253-0.93580.27660.5169-0.1192-0.4233-0.19470.41210.0567-0.07630.24030.17730.3186-11.946829.6184-52.2938
85.41511.9379-0.4957.14942.561710.6711-0.28880.8912-0.663-0.20620.4334-0.19161.4994-0.5809-0.14460.2612-0.1456-0.00780.3012-0.0860.148524.9917-5.8458-53.4451
93.4892-0.16480.59367.43411.28849.51840.2454-0.49580.37211.00570.32430.0584-1.1210.5364-0.56970.5212-0.12420.18190.1316-0.09430.31767.049633.8455-24.4372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 69
2X-RAY DIFFRACTION2B10 - 69
3X-RAY DIFFRACTION3C-1 - 69
4X-RAY DIFFRACTION4D8 - 69
5X-RAY DIFFRACTION5C - D300 - 369
6X-RAY DIFFRACTION6A70 - 212
7X-RAY DIFFRACTION7B70 - 210
8X-RAY DIFFRACTION8C70 - 210
9X-RAY DIFFRACTION9D70 - 210

+
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