[English] 日本語
Yorodumi
- PDB-6bsb: Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bsb
TitleCrystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
Components(Mucin-1) x 2
KeywordsSTRUCTURAL PROTEIN / SEA domain Autoproteolysis MUC1
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription coregulator activity / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Helix Hairpins - #600 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsNoguera, M.E. / Jakoncic, J. / Ermacora, M.R.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National University of Quilmes Argentina
ANPCYT Argentina
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: High-resolution structure of intramolecularly proteolyzed human mucin-1 SEA domain.
Authors: Noguera, M.E. / Jakoncic, J. / Ermacora, M.R.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 30, 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: Mucin-1
B: Mucin-1


Theoretical massNumber of molelcules
Total (without water)12,9312
Polymers12,9312
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-25 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.700, 43.700, 79.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Mucin-1 / MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma- ...MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma-associated mucin / Episialin / H23AG / Krebs von den Lungen-6 / KL-6 / PEMT / Peanut-reactive urinary mucin / PUM / Polymorphic epithelial mucin / PEM / Tumor-associated epithelial membrane antigen / EMA / Tumor-associated mucin


Mass: 6754.366 Da / Num. of mol.: 1 / Fragment: SEA domain, N-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC1, PUM / Production host: Escherichia coli (E. coli) / References: UniProt: P15941
#2: Protein Mucin-1 / MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma- ...MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma-associated mucin / Episialin / H23AG / Krebs von den Lungen-6 / KL-6 / PEMT / Peanut-reactive urinary mucin / PUM / Polymorphic epithelial mucin / PEM / Tumor-associated epithelial membrane antigen / EMA / Tumor-associated mucin


Mass: 6176.623 Da / Num. of mol.: 1 / Fragment: SEA domain, C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC1, PUM / Production host: Escherichia coli (E. coli) / References: UniProt: P15941
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 27.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Native crystals (see related entry) were used as seeds in a drop of 1:1 mix of the SeMet-derivative (9 mg/ml in 10 mM Tris-Cl, pH 7.4) and reservoir solution (0.1 M sodium acetate trihydrate ...Details: Native crystals (see related entry) were used as seeds in a drop of 1:1 mix of the SeMet-derivative (9 mg/ml in 10 mM Tris-Cl, pH 7.4) and reservoir solution (0.1 M sodium acetate trihydrate pH 4.6, 1.75 M sodium chloride, 0.2 M ammonium sulfate).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 24, 2014
RadiationMonochromator: Si (111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 22032 / % possible obs: 98.2 % / Redundancy: 6.832 % / Biso Wilson estimate: 19.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 1.022 / Net I/σ(I): 20.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.73.6690.4922.1933470.7530.57789.6
1.7-1.85.2170.3294.3929480.920.36799.7
1.8-1.97.7560.2438.1423810.9780.261100
1.9-27.9580.16912.1619030.9880.181100
2-2.27.8920.10619.0528340.9950.113100
2.2-2.47.8980.07924.2619810.9970.085100
2.4-2.57.8340.06428.757590.9980.069100
2.5-2.87.7960.05732.5817070.9980.061100
2.8-37.7440.04638.927620.9990.049100
3-3.57.5750.03745.1612790.9990.039100
3.5-47.5380.03252.157160.9990.034100
4-57.640.02855.9969710.03100
5-67.9320.02752.742940.9990.029100
6-97.9320.02655.063100.9990.028100
9-107.9350.02658.13310.9990.027100
10-127.7630.02662.12380.9990.028100
12-157.8440.02657.47320.9990.028100
15-207.0770.03160.43130.9990.033100

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2306refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.147 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 24.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 626 5.25 %RANDOM
Rwork0.1746 ---
obs0.177 11913 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.86 Å2 / Biso mean: 25.4238 Å2 / Biso min: 10.29 Å2
Refinement stepCycle: final / Resolution: 1.6→19.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 0 64 927
Biso mean---30.8 -
Num. residues----106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01903
X-RAY DIFFRACTIONf_angle_d0.8921223
X-RAY DIFFRACTIONf_chiral_restr0.053133
X-RAY DIFFRACTIONf_plane_restr0.007161
X-RAY DIFFRACTIONf_dihedral_angle_d14.079327
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 (%)
1.6001-1.7610.30281550.23352614276993
1.761-2.01560.24921630.185228102973100
2.0156-2.53850.22171360.177428773013100
2.5385-19.14870.20261720.16329863158100

+
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