[English] 日本語
Yorodumi
- PDB-6zyf: Notum_Ghrelin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zyf
TitleNotum_Ghrelin complex
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsSIGNALING PROTEIN / Notum Ghrelin
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
Chem-K4Q / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M000141/1 United Kingdom
CitationJournal: Mol Metab / Year: 2021
Title: Notum deacylates octanoylated ghrelin.
Authors: Zhao, Y. / Schuhmacher, L.N. / Roberts, M. / Kakugawa, S. / Bineva-Todd, G. / Howell, S. / O'Reilly, N. / Perret, C. / Snijders, A.P. / Vincent, J.P. / Jones, E.Y.
History
DepositionJul 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
B: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0998
Polymers87,1022
Non-polymers9976
Water1,00956
1
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9883
Polymers43,5511
Non-polymers4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1125
Polymers43,5511
Non-polymers5614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.418, 184.072, 61.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 86 through 194 or resid 199 through 418 or resid 432 through 451 or resid 501))
21(chain B and (resid 86 through 143 or (resid 144...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain A and (resid 86 through 194 or resid 199 through 418 or resid 432 through 451 or resid 501))AA86 - 1949 - 117
12GLUGLULEULEU(chain A and (resid 86 through 194 or resid 199 through 418 or resid 432 through 451 or resid 501))AA199 - 418122 - 341
13CYSCYSTHRTHR(chain A and (resid 86 through 194 or resid 199 through 418 or resid 432 through 451 or resid 501))AA432 - 451355 - 374
14NAGNAGNAGNAG(chain A and (resid 86 through 194 or resid 199 through 418 or resid 432 through 451 or resid 501))AC501
21ASNASNMETMET(chain B and (resid 86 through 143 or (resid 144...BB86 - 1439 - 66
22ARGARGARGARG(chain B and (resid 86 through 143 or (resid 144...BB14467
23ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374
24ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374
25ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374
26ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374
27ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374
28ASNASNTHRTHR(chain B and (resid 86 through 143 or (resid 144...BB86 - 4519 - 374

-
Components

#1: Protein Palmitoleoyl-protein carboxylesterase NOTUM / hNOTUM


Mass: 43551.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human)
References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-K4Q / [(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate


Mass: 215.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H21NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 7 / Details: 0.1 M Hepes pH 7.0 0.1 M KCl 15% PEG MME 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.19→92.04 Å / Num. obs: 45353 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 10.3
Reflection shellResolution: 2.19→2.23 Å / Num. unique obs: 2207 / CC1/2: 0.53 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZQ

4uzq


Resolution: 2.19→92.04 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2257 5.05 %
Rwork0.231 42406 -
obs0.232 44663 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.98 Å2 / Biso mean: 56.5252 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: final / Resolution: 2.19→92.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5613 0 61 56 5730
Biso mean--62.74 42.55 -
Num. residues----701
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3269X-RAY DIFFRACTION12.921TORSIONAL
12B3269X-RAY DIFFRACTION12.921TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.240.37051440.38282497264195
2.24-2.290.40011570.36322564272197
2.29-2.350.35871170.35872577269498
2.35-2.410.35941460.33732599274598
2.41-2.480.30031330.30882594272798
2.48-2.560.34561400.30112626276699
2.56-2.650.30771220.28432622274499
2.65-2.760.3061450.27712606275199
2.76-2.880.25311560.26792643279999
2.88-3.040.30161320.26722671280399
3.04-3.230.27531170.254626822799100
3.23-3.480.25271460.233526922838100
3.48-3.830.22681470.215126842831100
3.83-4.380.2461500.188527102860100
4.38-5.520.19031460.165627482894100
5.52-92.040.19051590.182728913050100
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)
10.0567-0.01550.01830.08260.03980.0373-0.1751-0.22090.52120.1289-0.0643-0.3105-0.08460.0277-0.13770.4847-0.6144-0.12440.2339-0.8531-0.1849-54.539829.4557-19.9132
20.3584-0.11190.26860.35440.30570.21510.5241-0.16450.5835-0.1135-0.0759-0.4647-0.2936-0.40070.35390.2005-0.6057-0.26240.3707-0.310.0909-53.457521.098-22.9363
31.35710.52040.21821.2422-0.24930.6150.0370.03790.0436-0.1238-0.00490.02050.1374-0.0960.02670.3638-0.19240.01270.3459-0.02040.2319-60.482412.5313-34.2413
40.48120.45570.22220.5160.25050.032-0.44910.4788-0.0806-0.24650.4860.10380.2061-0.4403-0.0020.3544-0.22910.04470.4315-0.11040.1584-33.20731.285-12.8616
50.19740.02950.1440.11350.00560.0857-0.12650.1349-0.0472-0.12140.1930.04850.2979-0.20950.00570.3463-0.1780.05210.3911-0.07110.2909-39.367828.6198-3.6876
60.4116-0.06110.15340.232-0.0640.1165-0.45390.4570.4345-0.21210.37980.0891-0.0163-0.0444-0.05370.3656-0.17220.03160.37190.05890.3568-29.920340.4688-11.3976
70.48960.38390.03540.15110.0294-0.1161-0.17810.14790.07780.06270.2205-0.35670.06590.0955-0.01470.2383-0.00890.02640.1962-0.06110.3657-20.921332.3196-3.1246
80.49780.34320.10660.3284-0.11680.3193-0.18320.0118-0.39530.06810.1498-0.58340.01140.15480.0040.24350.01640.0560.2704-0.03990.5812-14.795525.5621-0.5157
90.22260.11580.12450.0304-0.00680.1517-0.0418-1.2924-0.56730.6392-0.11590.07030.2987-0.0046-0.0240.5353-0.0557-0.10220.40920.21970.5452-27.602221.809413.2791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 107 )A86 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 159 )A108 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 451 )A160 - 451
4X-RAY DIFFRACTION4chain 'B' and (resid 86 through 147 )B86 - 147
5X-RAY DIFFRACTION5chain 'B' and (resid 148 through 185 )B148 - 185
6X-RAY DIFFRACTION6chain 'B' and (resid 186 through 224 )B186 - 224
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 286 )B225 - 286
8X-RAY DIFFRACTION8chain 'B' and (resid 287 through 394 )B287 - 394
9X-RAY DIFFRACTION9chain 'B' and (resid 395 through 451 )B395 - 451

+
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