[English] 日本語
Yorodumi
- PDB-7tl6: Murine meteorin N-terminal CUB domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tl6
TitleMurine meteorin N-terminal CUB domain
ComponentsMeteorin
KeywordsSIGNALING PROTEIN / meteorin / CUB domain / neurotrophic factor
Function / homologyMeteorin / radial glial cell differentiation / glial cell differentiation / positive regulation of axonogenesis / axonogenesis / hormone activity / extracellular space / Meteorin
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQuan, C. / Arndt, J.W. / Pepinsky, B. / Gong, B.J. / Dolnikova, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Identification and structure determination of stable domains of meteorin and meteorin-like
Authors: Quan, C. / Arndt, J.W. / Pepinsky, R.B. / Gong, B.J. / Dolnikova, J.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Meteorin
B: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7803
Polymers29,6842
Non-polymers961
Water905
1
A: Meteorin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9382
Polymers14,8421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Meteorin


Theoretical massNumber of molelcules
Total (without water)14,8421
Polymers14,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.508, 48.508, 191.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 5 or (resid 6...
21(chain B and (resid 1 through 47 or resid 54...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 5 or (resid 6...A1 - 5
121(chain A and (resid 1 through 5 or (resid 6...A6
131(chain A and (resid 1 through 5 or (resid 6...A1 - 130
211(chain B and (resid 1 through 47 or resid 54...B1 - 47
221(chain B and (resid 1 through 47 or resid 54...B54 - 63
231(chain B and (resid 1 through 47 or resid 54...B64
241(chain B and (resid 1 through 47 or resid 54...B1 - 130
251(chain B and (resid 1 through 47 or resid 54...B1 - 130
261(chain B and (resid 1 through 47 or resid 54...B1 - 130
271(chain B and (resid 1 through 47 or resid 54...B1 - 130

-
Components

#1: Protein Meteorin / Hypoxia/reoxygenation regulatory factor


Mass: 14841.752 Da / Num. of mol.: 2 / Fragment: CUB domain (UNP residues 22-155)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Metrn, Hyrac / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8C1Q4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl, pH 8.5, 200 mM lithium sulfate, 31% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.9 Å / Num. obs: 10896 / % possible obs: 99.76 % / Redundancy: 24 % / CC1/2: 0.986 / Rpim(I) all: 0.037 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.29 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1013 / CC1/2: 0.43 / Rpim(I) all: 0.64 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.76 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 536 4.92 %
Rwork0.2516 10352 -
obs0.2537 10888 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.82 Å2 / Biso mean: 63.7995 Å2 / Biso min: 29.2 Å2
Refinement stepCycle: final / Resolution: 2.3→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 5 5 1760
Biso mean--72.73 47.18 -
Num. residues----239
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A936X-RAY DIFFRACTION15.054TORSIONAL
12B936X-RAY DIFFRACTION15.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.530.35761140.3042506262099
2.53-2.90.32961200.293125352655100
2.9-3.650.2911450.252425642709100
3.65-33.760.27831570.234527472904100
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)
19.44760.3975-1.5524.12590.61964.52560.0381-0.7980.47640.07710.19730.0424-0.5592-0.2336-0.19690.30270.03410.05140.45340.01020.368312.0458-6.074422.7074
24.45143.10351.41012.53971.74581.963-0.13020.5309-0.3547-0.47240.2431-0.45330.06970.2106-0.16180.3030.06810.06750.46450.00990.377519.3224-8.905611.714
38.75370.56890.26534.30850.26435.5606-0.074-0.05790.4522-0.01890.1870.1234-0.17740.0689-0.1290.30070.00930.07550.47640.11730.29117.7226-5.461112.2396
43.92631.86060.68292.00030.16480.96260.233-0.19890.5347-0.0012-0.321-0.5314-0.0728-0.10440.36660.92540.1184-0.07640.49630.0920.66734.2077-0.8562-18.0451
56.2254-0.09292.94461.2757-0.9432.967-0.39990.46781.2261-0.1089-0.3116-0.4737-0.37650.86120.5590.5402-0.0345-0.03170.45980.08310.51348.3578-7.7249-12.938
69.4749-0.3501-0.44236.86141.49264.9446-0.1995-0.8601-0.053-0.9180.483-0.0582-0.31390.3511-0.27730.56250.0234-0.09490.3782-0.02250.49454.2897-16.2565-9.7864
723.71791.8495.52145.36075.5616-1.2691-0.46872.86360.4206-0.6972-1.9331.07031.05352.41871.33850.1314-0.23550.62340.17281.1711-2.201-15.1512-3.8099
81.86231.61681.14213.04910.81214.3060.0167-0.4934-0.5837-0.27740.0735-0.0868-0.4454-0.1569-0.14530.52230.04910.06160.4635-0.00370.41813.8914-14.1999-12.2593
93.03160.03253.83022.43470.25444.843-1.0645-0.9739-0.11550.11040.5764-0.2904-1.27260.19050.37160.4201-0.0074-0.0490.4809-0.03910.478910.0686-6.8455-5.5589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )A1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 84 )A41 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 130 )A85 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )B1 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 62 )B22 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 84 )B63 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 93 )B85 - 93
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 119 )B94 - 119
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 130 )B120 - 130

+
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