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- PDB-3lra: Structural Basis for Assembling a Human Tripartite Complex Dlg1-M... -

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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


protein localization to basolateral plasma membrane / regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / morphogenesis of an epithelial sheet / membrane raft organization / hard palate development ...protein localization to basolateral plasma membrane / regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / morphogenesis of an epithelial sheet / membrane raft organization / hard palate development / maintenance of epithelial cell apical/basal polarity / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / guanylate kinase activity / NrCAM interactions / regulation of sodium ion transmembrane transport / Dopamine Neurotransmitter Release Cycle / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / Synaptic adhesion-like molecules / protein localization to adherens junction / cell projection membrane / smooth muscle tissue development / bicellular tight junction assembly / positive regulation of potassium ion transport / neurotransmitter secretion / regulation of ventricular cardiac muscle cell action potential / amyloid precursor protein metabolic process / node of Ranvier / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / protein-containing complex localization / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / endothelial cell proliferation / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / regulation of myelination / Activation of Ca-permeable Kainate Receptor / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / positive regulation of actin filament polymerization / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / RHOG GTPase cycle / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / bicellular tight junction / intercalated disc / potassium channel regulator activity / lateral plasma membrane / RAC3 GTPase cycle / RAC2 GTPase cycle / phosphatase binding / signaling adaptor activity / T cell proliferation / negative regulation of T cell proliferation / RAC1 GTPase cycle / cytoskeletal protein binding / actin filament polymerization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / PDZ domain binding / protein localization to plasma membrane / positive regulation of protein-containing complex assembly / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / adherens junction / sarcolemma / neuromuscular junction / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / kinase binding / negative regulation of epithelial cell proliferation / cell-cell junction / protein transport / presynapse / cell junction / cell cortex
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 / L27 domain profile. / Polyubiquitination (PEST) N-terminal domain of MAGUK ...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. / Polyubiquitination (PEST) N-terminal domain of MAGUK / L27 domain superfamily / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / 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.

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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: 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

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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

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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

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