[English] 日本語
Yorodumi
- PDB-8frr: Wild-type myocilin olfactomedin domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8frr
TitleWild-type myocilin olfactomedin domain
ComponentsMyocilin, C-terminal fragment
KeywordsPROTEIN BINDING / Myocilin / olfactomedin / glaucoma / beta-propeller
Function / homology
Function and homology information


skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization ...skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / node of Ranvier / frizzled binding / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization / negative regulation of cell-matrix adhesion / 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 / positive regulation of JNK cascade / bone development / mitochondrial intermembrane space / cilium / receptor tyrosine kinase binding / 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
Similarity search - Function
Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsMa, M.T. / Lieberman, R.L. / Huard, D.J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)10R01EY021205 United States
CitationJournal: Nat Commun / Year: 2024
Title: Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming beta-propeller.
Authors: Saccuzzo, E.G. / Mebrat, M.D. / Scelsi, H.F. / Kim, M. / Ma, M.T. / Su, X. / Hill, S.E. / Rheaume, E. / Li, R. / Torres, M.P. / Gumbart, J.C. / Van Horn, W.D. / Lieberman, R.L.
History
DepositionJan 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myocilin, C-terminal fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4124
Polymers29,2571
Non-polymers1553
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.468, 50.527, 50.873
Angle α, β, γ (deg.)90.00, 96.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Myocilin, C-terminal fragment / / Myocilin 35 kDa N-terminal fragment


Mass: 29256.824 Da / Num. of mol.: 1 / Fragment: olfactomedin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOC, GLC1A, TIGR / Production host: Escherichia coli (E. coli) / References: UniProt: Q99972
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 5% PEG 8000, 0.05 M magnesium formate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→27.91 Å / Num. obs: 62921 / % possible obs: 95.26 % / Redundancy: 6.4 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08769 / Net I/σ(I): 16.41
Reflection shellResolution: 1.27→1.315 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.5015 / Num. unique obs: 5951 / % possible all: 91.44

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→27.91 Å / SU ML: 0.09 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 15.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1553 2001 3.19 %
Rwork0.1395 --
obs0.14 62786 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 8 282 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_d1.582
X-RAY DIFFRACTIONf_dihedral_angle_d6.616335
X-RAY DIFFRACTIONf_chiral_restr0.118350
X-RAY DIFFRACTIONf_plane_restr0.014418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.30.2021280.18773987X-RAY DIFFRACTION88
1.3-1.340.20491490.17314244X-RAY DIFFRACTION93
1.34-1.370.17731290.16714256X-RAY DIFFRACTION94
1.37-1.420.19971430.16034266X-RAY DIFFRACTION94
1.42-1.470.19081420.14684329X-RAY DIFFRACTION95
1.47-1.530.15821450.13744211X-RAY DIFFRACTION92
1.53-1.60.15831430.13064324X-RAY DIFFRACTION96
1.6-1.680.15761450.12854417X-RAY DIFFRACTION96
1.68-1.790.13611460.12614377X-RAY DIFFRACTION97
1.79-1.930.13961460.12464454X-RAY DIFFRACTION97
1.93-2.120.13621400.12494327X-RAY DIFFRACTION95
2.12-2.430.14051430.13064515X-RAY DIFFRACTION98
2.43-3.060.14981510.14924551X-RAY DIFFRACTION99
3.06-3.060.16171510.14264527X-RAY DIFFRACTION97
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)
12.94850.46530.39640.98660.0430.9127-0.0673-0.0382-0.292-0.01860.04660.01280.0818-0.0647-0.00570.1098-0.01980.00030.0826-0.00380.1338-13.2344-12.6017-1.2836
20.9223-0.1291-0.14651.35870.87712.29770.03420.051-0.01460.0094-0.0488-0.00190.12780.00560.00770.08130.0038-0.00220.0827-0.00290.0936-0.9559-6.5764-10.9878
31.0366-0.4767-0.12931.21710.19221.19260.034-0.03970.02930.001-0.0433-0.10950.00790.12760.01360.0879-0.0040.00420.1001-0.00070.10333.8281-3.2599-9.5393
41.1217-0.0011-0.68520.75310.12730.66990.20430.08830.2646-0.1193-0.0893-0.1749-0.15270.0331-0.05540.1280.00540.03740.13270.03060.14792.78572.952-14.6558
51.3825-0.6699-0.47361.20030.23030.95020.14820.25910.1645-0.2481-0.1336-0.0887-0.1437-0.0552-0.01230.13250.0230.01030.12690.02880.1013-6.924.6431-20.3253
60.7727-0.207-0.42190.7382-0.19310.97260.03930.07840.0832-0.04-0.05030.0155-0.0269-0.07390.0060.08210.0091-0.01060.09690.00340.0943-14.67322.001-12.0374
71.51270.2495-0.66681.52450.36711.8510.09710.43640.1073-0.2333-0.18840.1648-0.152-0.2410.01610.12710.0604-0.03330.19930.03470.1137-19.51825.1011-19.8221
81.3004-0.1054-0.27850.9548-0.06130.92780.04880.0858-0.0004-0.0158-0.03170.0904-0.0109-0.1605-0.00380.06550.0053-0.00440.1017-0.00640.0949-22.11560.2475-6.907
90.554-0.24320.40910.2252-0.52581.33510.01030.1174-0.1028-0.03080.03860.12310.0696-0.2742-0.08320.1265-0.0126-0.0050.196-0.00490.1674-27.988-5.8212-4.7366
101.02260.2810.19421.49840.49222.18840.0062-0.0317-0.08850.0775-0.04040.0030.0674-0.06310.00110.0906-0.00010.00220.08670.00180.1071-10.5025-6.1086-1.5835
112.72480.93550.59371.30790.18941.36690.0587-0.0719-0.23510.0554-0.05850.03280.1022-0.09490.00330.0812-0.0059-0.00420.0627-0.00370.102-9.8675-9.1215-2.0369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 244 through 259 )
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 284 )
3X-RAY DIFFRACTION3chain 'A' and (resid 285 through 309 )
4X-RAY DIFFRACTION4chain 'A' and (resid 310 through 327 )
5X-RAY DIFFRACTION5chain 'A' and (resid 328 through 369 )
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 392 )
7X-RAY DIFFRACTION7chain 'A' and (resid 393 through 412 )
8X-RAY DIFFRACTION8chain 'A' and (resid 413 through 454 )
9X-RAY DIFFRACTION9chain 'A' and (resid 455 through 467 )
10X-RAY DIFFRACTION10chain 'A' and (resid 468 through 484 )
11X-RAY DIFFRACTION11chain 'A' and (resid 485 through 502 )

+
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