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- PDB-6zyf: Notum_Ghrelin complex -

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Basic information

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


protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / C-type glycerophospholipase activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway ...protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / C-type glycerophospholipase activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Wnt signaling pathway / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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