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- PDB-3uit: Overall structure of Patj/Pals1/Mals complex -

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Basic information

Entry
Database: PDB / ID: 3uit
TitleOverall structure of Patj/Pals1/Mals complex
ComponentsInaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
KeywordsCELL ADHESION / L27 domain / CELL POLARIZATION
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / subapical complex / MPP7-DLG1-LIN7 complex / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / regulation of synaptic assembly at neuromuscular junction / morphogenesis of an epithelial sheet / tight junction assembly ...RHO GTPases Activate Rhotekin and Rhophilins / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / subapical complex / MPP7-DLG1-LIN7 complex / myelin assembly / establishment or maintenance of polarity of embryonic epithelium / regulation of synaptic assembly at neuromuscular junction / morphogenesis of an epithelial sheet / tight junction assembly / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / establishment of apical/basal cell polarity / Dopamine Neurotransmitter Release Cycle / microtubule organizing center organization / lateral loop / Schmidt-Lanterman incisure / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / cell-cell junction assembly / neurotransmitter secretion / tight junction / apical junction complex / generation of neurons / synaptic vesicle transport / central nervous system neuron development / exocytosis / positive regulation of epithelial cell migration / bicellular tight junction / postsynaptic density, intracellular component / endoplasmic reticulum-Golgi intermediate compartment membrane / regulation of microtubule cytoskeleton organization / protein localization to plasma membrane / adherens junction / PDZ domain binding / postsynaptic density membrane / cerebral cortex development / apical part of cell / cell-cell junction / protein transport / presynapse / regulation of protein localization / perikaryon / protein-macromolecule adaptor activity / basolateral plasma membrane / gene expression / apical plasma membrane / protein domain specific binding / axon / synapse / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #460 / de novo design (two linked rop proteins) - #360 / Protein lin-7 / : / L27-N / MPP5, SH3 domain / L27_N / L27-2 / L27_2 / L27 domain, C-terminal ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #460 / de novo design (two linked rop proteins) - #360 / Protein lin-7 / : / L27-N / MPP5, SH3 domain / L27_N / L27-2 / L27_2 / L27 domain, C-terminal / L27 domain / : / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / de novo design (two linked rop proteins) / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / InaD-like protein / InaD-like protein / Protein PALS1 / Protein lin-7 homolog B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsZhang, J. / Yang, X. / Long, J. / Shen, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of an L27 domain heterotrimer from cell polarity complex Patj/Pals1/Mals2 reveals mutually independent L27 domain assembly mode
Authors: Zhang, J. / Yang, X. / Wang, Z. / Zhou, H. / Xie, X. / Shen, Y. / Long, J.
History
DepositionNov 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
B: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
C: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
D: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,60624
Polymers119,4254
Non-polymers1,18120
Water15,565864
1
A: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3299
Polymers29,8561
Non-polymers4728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1516
Polymers29,8561
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9743
Polymers29,8561
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1516
Polymers29,8561
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.194, 145.194, 202.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-222-

ARG

21B-877-

HOH

31C-911-

HOH

41D-680-

HOH

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Components

#1: Protein
InaD-like protein, MAGUK p55 subfamily member 5, Protein lin-7 homolog B / Inadl protein / Channel-interacting PDZ domain-containing protein / Pals1-associated tight junction ...Inadl protein / Channel-interacting PDZ domain-containing protein / Pals1-associated tight junction protein / Protein associated to tight junctions / Lin-7B / Mammalian lin-seven protein 2 / MALS-2 / Vertebrate lin-7 homolog 2 / Veli-2


Mass: 29856.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Chimera of L27 domains of InaD-like protein (UNP residues 1-68) from Mouse, LINKER (LEVLFQGP), MAGUK p55 subfamily member 5 (UNP residues 119-232) from Human, LINKER (GGGLEVFQGP), Protein ...Details: Chimera of L27 domains of InaD-like protein (UNP residues 1-68) from Mouse, LINKER (LEVLFQGP), MAGUK p55 subfamily member 5 (UNP residues 119-232) from Human, LINKER (GGGLEVFQGP), Protein lin-7 homolog B (UNP residues 3-66) from Rat
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
References: UniProt: Q63ZW7, UniProt: Q8N3R9, UniProt: Q9Z252, UniProt: F1MAD2*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9791
SYNCHROTRONSSRF BL17U20.9791
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 23, 2010
MARMOSAIC 225 mm CCD2CCDSep 9, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 79261 / % possible obs: 87.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20.2 % / Biso Wilson estimate: 29.21 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.081 / Net I/σ(I): 36.2
Reflection shellResolution: 2.05→2.12 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→38.863 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8479 / SU ML: 0.22 / σ(F): 2 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 3879 5.03 %RANDOM
Rwork0.1797 ---
all0.1818 79223 --
obs0.1817 77147 97.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.246 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 224.64 Å2 / Biso mean: 41.2893 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.5912 Å2-0 Å2-0 Å2
2--0.5912 Å20 Å2
3----1.1824 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8103 0 80 864 9047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078293
X-RAY DIFFRACTIONf_angle_d1.00611197
X-RAY DIFFRACTIONf_dihedral_angle_d16.4943167
X-RAY DIFFRACTIONf_chiral_restr0.0671311
X-RAY DIFFRACTIONf_plane_restr0.0041476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0499-2.12310.24833210.1926681092
2.1231-2.20810.23033920.1805698694
2.2081-2.30860.2553760.1875712996
2.3086-2.43030.23873490.1788723397
2.4303-2.58260.24733990.1884724498
2.5826-2.78190.24944130.1946735399
2.7819-3.06180.27183950.2099742199
3.0618-3.50460.24074130.18657513100
3.5046-4.41440.17294160.15077611100
4.4144-38.86990.19584050.17697968100
Refinement TLS params.Method: refined / Origin x: -43.3383 Å / Origin y: 27.7285 Å / Origin z: 34.3325 Å
111213212223313233
T0.1256 Å20.015 Å20.0112 Å2-0.0936 Å20.0524 Å2--0.1306 Å2
L0.3796 °20.0676 °2-0.0309 °2-0.4645 °20.0202 °2--0.6063 °2
S-0.0157 Å °-0.0296 Å °-0.0688 Å °-0.0644 Å °-0.033 Å °-0.0482 Å °0.0218 Å °-0.0117 Å °0.0458 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 263
2X-RAY DIFFRACTION1allB9 - 261
3X-RAY DIFFRACTION1allC9 - 263
4X-RAY DIFFRACTION1allD8 - 264
5X-RAY DIFFRACTION1allB - C1 - 912
6X-RAY DIFFRACTION1allD1428
7X-RAY DIFFRACTION1allB1428
8X-RAY DIFFRACTION1allA1428
9X-RAY DIFFRACTION1allB266 - 1428
10X-RAY DIFFRACTION1allB267 - 1428
11X-RAY DIFFRACTION1allC1428
12X-RAY DIFFRACTION1allA266 - 1428
13X-RAY DIFFRACTION1allB268 - 1428
14X-RAY DIFFRACTION1allA267 - 1428
15X-RAY DIFFRACTION1allC266 - 1428
16X-RAY DIFFRACTION1allD266 - 1428
17X-RAY DIFFRACTION1allA268 - 1428
18X-RAY DIFFRACTION1allD267 - 1428
19X-RAY DIFFRACTION1allA269 - 1428
20X-RAY DIFFRACTION1allA270 - 1428
21X-RAY DIFFRACTION1allA271 - 1428
22X-RAY DIFFRACTION1allA272 - 1428
23X-RAY DIFFRACTION1allD268 - 1428
24X-RAY DIFFRACTION1allD269 - 1428
25X-RAY DIFFRACTION1allB269 - 1428

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