[English] 日本語
Yorodumi
- PDB-5vr2: mouse myocilin leucine zipper C-terminal 7 heptad repeat -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vr2
Titlemouse myocilin leucine zipper C-terminal 7 heptad repeat
ComponentsMyocilin
KeywordsSIGNALING PROTEIN / coiled coil / disulfide bond / extracellular matrix / trabecular meshwork / leucine zipper
Function / homology
Function and homology information


: / mesaxon / skeletal muscle hypertrophy / : / clustering of voltage-gated sodium channels / myosin light chain binding / myelin sheath abaxonal region / Schmidt-Lanterman incisure / myelination in peripheral nervous system / node of Ranvier ...: / mesaxon / skeletal muscle hypertrophy / : / clustering of voltage-gated sodium channels / myosin light chain binding / myelin sheath abaxonal region / Schmidt-Lanterman incisure / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / negative regulation of cell-matrix adhesion / positive regulation of mitochondrial depolarization / ERBB2-ERBB3 signaling pathway / positive regulation of focal adhesion assembly / regulation of MAPK cascade / fibronectin binding / positive regulation of substrate adhesion-dependent cell spreading / rough endoplasmic reticulum / positive regulation of stress fiber assembly / bone development / mitochondrial intermembrane space / receptor tyrosine kinase binding / cilium / osteoblast differentiation / neuron projection development / cytoplasmic vesicle / collagen-containing extracellular matrix / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / Golgi apparatus / endoplasmic reticulum / signal transduction / extracellular space / extracellular exosome / metal ion binding / cytoplasm
Similarity search - Function
Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.922 Å
AuthorsLieberman, R.L. / Hill, S.E.
CitationJournal: Structure / Year: 2017
Title: Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin.
Authors: Hill, S.E. / Nguyen, E. / Donegan, R.K. / Patterson-Orazem, A.C. / Hazel, A. / Gumbart, J.C. / Lieberman, R.L.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myocilin
B: Myocilin
C: Myocilin
D: Myocilin


Theoretical massNumber of molelcules
Total (without water)23,8344
Polymers23,8344
Non-polymers00
Water3,207178
1
A: Myocilin
B: Myocilin


Theoretical massNumber of molelcules
Total (without water)11,9172
Polymers11,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-27 kcal/mol
Surface area7330 Å2
MethodPISA
2
C: Myocilin
D: Myocilin


Theoretical massNumber of molelcules
Total (without water)11,9172
Polymers11,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-27 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.129, 48.746, 55.798
Angle α, β, γ (deg.)90.00, 105.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-247-

HOH

21B-256-

HOH

31B-259-

HOH

41C-233-

HOH

51C-238-

HOH

-
Components

#1: Protein/peptide
Myocilin / Trabecular meshwork-induced glucocorticoid response protein


Mass: 5958.507 Da / Num. of mol.: 4 / Fragment: UNP residues 122-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myoc, Tigr / Production host: Escherichia coli (E. coli) / References: UniProt: O70624
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M ammonium acetate, 0.1 M BisTris pH 5.5, and 17% PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.881 Å / Num. obs: 23662 / % possible obs: 97.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.05 / Rrim(I) all: 0.129 / Χ2: 1.322 / Net I/σ(I): 6.6 / Num. measured all: 142081
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.732.90.6520.3670.3820.7610.54780.7
1.73-1.763.50.740.7240.3960.8440.63585.8
1.76-1.7940.7360.7990.3670.8260.48491.1
1.79-1.834.50.710.8080.3360.7880.53696
1.83-1.874.90.5480.9150.2520.6060.56498.3
1.87-1.915.30.5430.9320.2430.5960.571100
1.91-1.965.80.4860.940.210.530.593100
1.96-2.026.10.3880.9630.1660.4230.653100
2.02-2.076.30.3350.9730.1420.3650.74100
2.07-2.146.40.2560.9840.1070.2770.826100
2.14-2.226.50.2220.9840.0930.2410.918100
2.22-2.316.60.1950.9880.0810.2121.037100
2.31-2.416.90.180.9910.0740.1951.158100
2.41-2.5470.1730.9920.0710.1871.222100
2.54-2.77.20.150.9940.0610.1621.402100
2.7-2.917.20.1280.9940.0520.1381.674100
2.91-3.27.10.1090.9940.0450.1182.03100
3.2-3.6670.0850.9960.0350.0922.43100
3.66-4.616.90.0690.9950.0290.0752.744100
4.61-506.60.0740.9950.0330.0812.92299.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
SERGUIdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
AMPLEphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.922→41.881 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 1616 9.94 %
Rwork0.1868 --
obs0.192 16261 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.922→41.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 178 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061649
X-RAY DIFFRACTIONf_angle_d0.7452203
X-RAY DIFFRACTIONf_dihedral_angle_d8.0471188
X-RAY DIFFRACTIONf_chiral_restr0.033237
X-RAY DIFFRACTIONf_plane_restr0.003310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9219-1.97840.30411100.2386991X-RAY DIFFRACTION78
1.9784-2.04230.32261220.21821146X-RAY DIFFRACTION91
2.0423-2.11530.26981290.21311201X-RAY DIFFRACTION94
2.1153-2.20.27341340.19551194X-RAY DIFFRACTION96
2.2-2.30010.24991370.19141243X-RAY DIFFRACTION98
2.3001-2.42130.28791370.20161241X-RAY DIFFRACTION99
2.4213-2.5730.23041390.20891269X-RAY DIFFRACTION100
2.573-2.77160.26571370.19571240X-RAY DIFFRACTION99
2.7716-3.05050.2631420.19491282X-RAY DIFFRACTION100
3.0505-3.49170.23721420.18511271X-RAY DIFFRACTION100
3.4917-4.39840.18361420.15341279X-RAY DIFFRACTION100
4.3984-41.89060.22811450.18671288X-RAY DIFFRACTION98
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)
12.4735-4.4682.56548.3663-4.84892.7468-0.3797-0.22210.01980.9963-0.326-0.5978-0.97480.86120.87550.4047-0.0799-0.04910.6409-0.08240.3489-6.098419.008689.6723
26.86332.05015.40342.09952.78155.5467-0.2262-0.00730.2414-0.0608-0.11490.0751-0.2797-0.21970.33010.2145-0.0010.00090.1782-0.0190.2432-23.395914.142158.067
36.1512.65962.49798.93246.00226.91560.1197-0.14940.12880.49650.23150.0375-0.10170.2493-0.2660.298-0.0517-0.00780.56510.05170.2394-15.281814.40290.5066
43.52240.05721.06140.9050.9552.383-0.1450.2281-0.32640.0370.02740.06250.19670.12680.17170.1733-0.01550.01670.1527-0.02030.2498-20.97656.291455.5472
59.21844.2884-6.04697.514-2.53824.04210.0625-1.4397-0.77430.4791-0.5189-0.1254-0.31250.25320.26840.29320.0353-0.05150.8598-0.010.2977-32.3621-14.827583.7515
69.10172.8823-4.34443.9162-1.96124.55920.12660.03870.4179-0.00350.0479-0.065-0.58670.4628-0.42860.2437-0.0033-0.06860.32490.0030.305-10.141-5.778956.9289
75.8719-3.9822-6.04882.80894.15226.2896-0.7547-0.0144-0.33860.59260.03080.48450.2945-0.38450.73660.3224-0.0006-0.00450.58730.11750.3881-41.8474-20.294181.0796
86.23252.0211-2.95961.406-1.15155.6918-0.2727-0.2739-0.706-0.08160.0477-0.24890.23270.4482-0.20470.24830.0921-0.03150.19520.0260.3182-11.512-14.355762.3105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 122:132)
2X-RAY DIFFRACTION2(chain A and resid 133:171)
3X-RAY DIFFRACTION3(chain B and resid 122:137)
4X-RAY DIFFRACTION4(chain B and resid 138:171)
5X-RAY DIFFRACTION5(chain C and resid 122:141)
6X-RAY DIFFRACTION6(chain C and resid 142:171)
7X-RAY DIFFRACTION7(chain D and resid 122:132)
8X-RAY DIFFRACTION8(chain D and resid 133:171)

+
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://pdbjlvh1.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