[English] 日本語
Yorodumi
- PDB-3lra: Structural Basis for Assembling a Human Tripartite Complex Dlg1-M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lra
TitleStructural Basis for Assembling a Human Tripartite Complex Dlg1-MPP7-Mals3
ComponentsDisks large homolog 1, MAGUK p55 subfamily member 7, Protein lin-7 homolog C
KeywordsMEMBRANE PROTEIN / Tripartite Complex / L27 tetramer / Cell junction / Cell membrane / Endoplasmic reticulum / Host-virus interaction / Postsynaptic cell membrane / SH3 domain / Synapse / Tight junction / Exocytosis / Protein transport / Synaptosome / Transport
Function / homology
Function and homology information


L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / regulation of synaptic assembly at neuromuscular junction / morphogenesis of an epithelial sheet / membrane raft organization / establishment of centrosome localization / hard palate development ...L27 domain binding / regulation of protein localization to synapse / regulation of potassium ion import / MPP7-DLG1-LIN7 complex / regulation of potassium ion export across plasma membrane / regulation of synaptic assembly at neuromuscular junction / morphogenesis of an epithelial sheet / membrane raft organization / establishment of centrosome localization / hard palate development / GMP kinase activity / structural constituent of postsynaptic density / membrane repolarization during ventricular cardiac muscle cell action potential / NrCAM interactions / astral microtubule organization / embryonic skeletal system morphogenesis / negative regulation of p38MAPK cascade / reproductive structure development / immunological synapse formation / lateral loop / receptor localization to synapse / myelin sheath abaxonal region / Dopamine Neurotransmitter Release Cycle / peristalsis / regulation of sodium ion transmembrane transport / smooth muscle tissue development / bicellular tight junction assembly / cortical microtubule organization / cell projection membrane / protein localization to adherens junction / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / neurotransmitter secretion / regulation of ventricular cardiac muscle cell action potential / positive regulation of potassium ion transport / Trafficking of AMPA receptors / protein-containing complex localization / node of Ranvier / amyloid precursor protein metabolic process / endothelial cell proliferation / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / cortical actin cytoskeleton organization / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / branching involved in ureteric bud morphogenesis / positive regulation of actin filament polymerization / synaptic vesicle transport / negative regulation of G1/S transition of mitotic cell cycle / receptor clustering / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Negative regulation of NMDA receptor-mediated neuronal transmission / RHOQ GTPase cycle / exocytosis / Unblocking of NMDA receptors, glutamate binding and activation / phosphoprotein phosphatase activity / Long-term potentiation / basement membrane / immunological synapse / RHOG GTPase cycle / intercalated disc / RAC2 GTPase cycle / RAC3 GTPase cycle / bicellular tight junction / lateral plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / potassium channel regulator activity / phosphatase binding / T cell proliferation / cytoskeletal protein binding / ionotropic glutamate receptor binding / signaling adaptor activity / negative regulation of T cell proliferation / actin filament polymerization / RAC1 GTPase cycle / Ras activation upon Ca2+ influx through NMDA receptor / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / actin filament organization / protein localization to plasma membrane / regulation of membrane potential / adherens junction / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein-containing complex assembly / synaptic membrane / postsynaptic density membrane / negative regulation of ERK1 and ERK2 cascade / neuromuscular junction / sarcolemma / cell-cell adhesion / cytoplasmic side of plasma membrane / kinase binding / negative regulation of epithelial cell proliferation / cell junction / protein transport
Similarity search - Function
MPP7, SH3 domain / Protein lin-7 / : / L27-1 / L27_1 / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain ...MPP7, SH3 domain / Protein lin-7 / : / L27-1 / L27_1 / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 1 / MAGUK p55 subfamily member 7 / Protein lin-7 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsYang, X. / Xie, X. / Shen, Y. / Long, J.
CitationJournal: Faseb J. / Year: 2010
Title: Structural basis for tandem L27 domain-mediated polymerization
Authors: Yang, X. / Xie, X. / Chen, L. / Zhou, H. / Wang, Z. / Zhao, W. / Tian, R. / Zhang, R. / Tian, C. / Long, J. / Shen, Y.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Disks large homolog 1, MAGUK p55 subfamily member 7, Protein lin-7 homolog C


Theoretical massNumber of molelcules
Total (without water)29,1641
Polymers29,1641
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.190, 153.190, 58.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Disks large homolog 1, MAGUK p55 subfamily member 7, Protein lin-7 homolog C / Dlg1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg / MPP7 / MALS-3 / Lin-7C / Mammalian ...Dlg1 / Synapse-associated protein 97 / SAP-97 / SAP97 / hDlg / MPP7 / MALS-3 / Lin-7C / Mammalian lin-seven protein 3 / Vertebrate lin-7 homolog 3 / Veli-3


Mass: 29164.166 Da / Num. of mol.: 1 / Fragment: L27 domain, L27 1/2 domain
Source method: isolated from a genetically manipulated source
Details: Structural Basis for Assembling a Tripartite Complex Dlg1-MPP7-Mals3
Source: (gene. exp.) Homo sapiens (human) / Gene: L27 domains of Dlg1, MPP7 and Mals3
Plasmid details: in-house-modified version of the pET32a vector (Novagen), in which the S-tag an d the thrombin recognition site were replaced by a sequence encoding a TEV prote ase cleavage site ...Plasmid details: in-house-modified version of the pET32a vector (Novagen), in which the S-tag an d the thrombin recognition site were replaced by a sequence encoding a TEV prote ase cleavage site (Glu-Asn-Leu-Tyr-Phe-Gln-Ser)
Plasmid: pET32a vector (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12959, UniProt: Q5T2T1, UniProt: Q9NUP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE L27 DOMAINS OF HUMAN DLG1 (TERMED AS L27HDLG1), HUMAN MPP7 (TERMED AS L27N AND L27C) AND HUMAN ...THE L27 DOMAINS OF HUMAN DLG1 (TERMED AS L27HDLG1), HUMAN MPP7 (TERMED AS L27N AND L27C) AND HUMAN MALS3 (TERMED AS L27HMALS3) WERE COVALENTLY LINKED TOGETHER BY PRECISSION PROTEASE CLEAVAGE SITE AS ONE SINGLE POLYPEPTIDE.
Sequence detailsTHE INTERNAL SEQUENCE LEVLFQGP ARE LINKER.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000, 0.2M MgCl2, 0.1M Guanidine HCl, 0.1M Tris-HCl, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A11
SYNCHROTRONAPS 19-ID20.9791
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDDec 30, 2008
ADSC QUANTUM 3152CCDNov 1, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
ReflectionResolution: 2.95→38.3 Å / Num. all: 8504 / Num. obs: 8045 / % possible obs: 95 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 14.8 % / Biso Wilson estimate: 1.2 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 25.7
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1047 / Rsym value: 0.435 / % possible all: 77.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→38.3 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 52963.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 472 5.6 %RANDOM
Rwork0.255 ---
all0.257 8504 --
obs0.255 8045 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.039 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 67.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.62 Å20 Å20 Å2
2--8.62 Å20 Å2
3----17.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.95→38.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 0 41 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.95→3.06 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 63 5.7 %
Rwork0.338 1047 -
obs-679 77.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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