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- PDB-6bsb: Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selen... -

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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 / localization / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 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).

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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

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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

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