[English] 日本語
Yorodumi
- PDB-5l0s: human POGLUT1 in complex with Factor VII EGF1 and UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l0s
Titlehuman POGLUT1 in complex with Factor VII EGF1 and UDP
Components
  • Coagulation factor VII
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase glycosyltransferase GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / regulation of gastrulation / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / regulation of gastrulation / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / serine-type peptidase complex / response to carbon dioxide / response to vitamin K / glucosyltransferase activity / circulatory system development / response to thyroxine / paraxial mesoderm development / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / protein O-linked glycosylation / response to cholesterol / axial mesoderm development / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of Notch signaling pathway / positive regulation of blood coagulation / positive regulation of TOR signaling / animal organ regeneration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / somitogenesis / Removal of aminoterminal propeptides from gamma-carboxylated proteins / gastrulation / serine-type peptidase activity / endomembrane system / BMAL1:CLOCK,NPAS2 activates circadian expression / protein processing / Golgi lumen / response to estrogen / circadian rhythm / blood coagulation / response to estradiol / : / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site ...Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Coagulation factor VII / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).
Authors: Li, Z. / Fischer, M. / Satkunarajah, M. / Zhou, D. / Withers, S.G. / Rini, J.M.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein O-glucosyltransferase 1
B: Coagulation factor VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,89510
Polymers46,5672
Non-polymers1,3288
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-33 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 76.920, 82.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 5 molecules AB

#1: Protein Protein O-glucosyltransferase 1 / CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes ...CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes relative protein / O-glucosyltransferase Rumi homolog / hRumi / Protein O-xylosyltransferase


Mass: 42077.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006
Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NBL1, Transferases; Glycosyltransferases; Hexosyltransferases, protein xylosyltransferase
#2: Protein/peptide Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 4489.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08709, coagulation factor VIIa
#3: 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.: 3
Source method: isolated from a genetically manipulated source
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

-
Non-polymers , 5 types, 382 molecules

#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 79619 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.61
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.68 / CC1/2: 0.653 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→44.001 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1588 3981 5 %0
Rwork0.1394 75631 --
obs0.1404 79612 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.35 Å2 / Biso mean: 29.8733 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.45→44.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 136 377 3753
Biso mean--29.26 37.73 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083484
X-RAY DIFFRACTIONf_angle_d1.0374741
X-RAY DIFFRACTIONf_chiral_restr0.077487
X-RAY DIFFRACTIONf_plane_restr0.007606
X-RAY DIFFRACTIONf_dihedral_angle_d16.2381322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46770.27431290.28092455258492
1.4677-1.48630.27431350.26042569270496
1.4863-1.50580.23331410.2472679282099
1.5058-1.52650.22661410.212226722813100
1.5265-1.54830.24481400.19892664280499
1.5483-1.57140.19571420.184627002842100
1.5714-1.59590.18481400.179926592799100
1.5959-1.62210.18331420.158626942836100
1.6221-1.65010.17191410.149826742815100
1.6501-1.68010.17211430.151927192862100
1.6801-1.71240.14771420.143726962838100
1.7124-1.74730.1751410.142726902831100
1.7473-1.78530.16021410.139326812822100
1.7853-1.82690.14651430.132727162859100
1.8269-1.87260.15041430.126427112854100
1.8726-1.92320.1571420.12227012843100
1.9232-1.97980.13941430.119927142857100
1.9798-2.04370.13851420.117226952837100
2.0437-2.11670.14321440.118327322876100
2.1167-2.20150.12631420.118127072849100
2.2015-2.30170.17131440.121327272871100
2.3017-2.4230.15731440.121127382882100
2.423-2.57480.14631430.12627252868100
2.5748-2.77360.14481450.127327512896100
2.7736-3.05260.13871440.130627442888100
3.0526-3.49420.14441470.13227752922100
3.4942-4.40160.1471450.12822764290999
4.4016-44.02150.18581520.16572879303198
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)
13.0889-0.7220.87071.014-0.52161.811-0.0797-0.3268-0.00960.08190.17820.1347-0.0321-0.4829-0.11850.1886-0.01440.020.29030.04140.13624.249230.678834.7269
22.1986-0.74930.27862.066-0.60383.98190.0087-0.0854-0.35890.0604-0.0368-0.14490.42930.3246-0.04740.20620.0813-0.06380.22010.030.306932.147814.142530.9797
32.49560.1531.0862.1973-0.00512.8180.0425-0.0756-0.13050.0528-0.0018-0.18160.03260.2421-0.0190.11420.0249-0.02450.15650.00250.158827.882222.032727.9822
41.3764-0.43380.41651.6933-0.57111.55760.05180.0356-0.0403-0.00470.0066-0.0565-0.01310.1154-0.02930.1102-0.0046-0.00880.1116-0.00370.124319.715227.477521.3237
52.3868-0.41980.4932.340.30662.38280.11950.1968-0.0611-0.1537-0.02570.1844-0.0187-0.176-0.0950.14250.0004-0.00940.18390.03160.13153.209331.83788.6209
62.6061.4862-0.24651.0390.61173.01430.19690.7825-0.4751-0.3282-0.13590.08470.21860.0461-0.06740.22930.0141-0.04990.2333-0.03450.16258.61424.49932.0898
71.6142-0.0610.16871.6156-0.01051.81650.05580.1746-0.0325-0.1750.04590.0922-0.0376-0.0273-0.090.1357-0.0003-0.01220.14510.00450.10589.39131.51699.9377
82.1683-0.35010.34271.0583-0.57971.57620.0144-0.045-0.10530.02890.11580.1417-0.0189-0.2589-0.12210.12080.0011-0.00060.15940.0340.14051.912730.571221.1033
99.2715-0.68883.73661.1922-0.53933.7791-0.2391-0.23560.57610.23260.13670.1234-0.5022-0.29430.13130.26380.0550.02370.15790.00810.19664.814942.044525.7739
102.4021-0.54070.21081.9414-0.24141.8238-0.0393-0.235-0.07650.26430.0323-0.40910.07360.3734-0.0190.16760.0132-0.06190.22480.00650.209230.09623.907834.6518
114.6822-2.3767-1.084.2242-0.19515.9624-0.04910.178-0.665-0.1245-0.1435-0.09150.77270.19320.13760.32130.04740.01260.2602-0.060.295526.163218.15027.2699
124.64942.44880.50592.50720.91386.45860.20560.32220.2486-0.5250.2964-1.2609-0.12281.2457-0.19390.34770.01520.14140.452-0.0710.548635.735126.62314.5462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 68 )A30 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 104 )A69 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 139 )A105 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 197 )A140 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 227 )A198 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 248 )A228 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 279 )A249 - 279
8X-RAY DIFFRACTION8chain 'A' and (resid 280 through 331 )A280 - 331
9X-RAY DIFFRACTION9chain 'A' and (resid 332 through 349 )A332 - 349
10X-RAY DIFFRACTION10chain 'A' and (resid 350 through 385 )A350 - 385
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 71 )B47 - 71
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 85 )B72 - 85

+
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