[English] 日本語
Yorodumi
- PDB-6q0u: Structure of the Erbin PDZ variant E-6a with a high-affinity C-te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q0u
TitleStructure of the Erbin PDZ variant E-6a with a high-affinity C-terminal peptide
Components
  • Erbin
  • peptide
KeywordsSIGNALING PROTEIN / peptide-phage display / protein engineering / PDZ domains / C-terminal peptide
Function / homology
Function and homology information


basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / negative regulation of NF-kappaB transcription factor activity / RHOC GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / response to muramyl dipeptide / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / protein targeting / RAC3 GTPase cycle / RAC2 GTPase cycle / Signaling by ERBB2 / RAC1 GTPase cycle / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / integrin-mediated signaling pathway / Signaling by ERBB2 TMD/JMD mutants / neuromuscular junction / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / nuclear membrane / response to lipopolysaccharide / cell adhesion / nuclear speck / signaling receptor binding / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSinger, A.U. / Teyra, J. / Ernst, A. / Sicheri, F. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93684 Canada
CitationJournal: Protein Sci. / Year: 2020
Title: Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities.
Authors: Teyra, J. / Ernst, A. / Singer, A. / Sicheri, F. / Sidhu, S.S.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Erbin
B: Erbin
C: peptide
D: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5056
Polymers22,3814
Non-polymers1242
Water2,414134
1
A: Erbin
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3154
Polymers11,1912
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area5810 Å2
MethodPISA
2
B: Erbin
D: peptide


Theoretical massNumber of molelcules
Total (without water)11,1912
Polymers11,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.590, 38.090, 38.450
Angle α, β, γ (deg.)83.04, 74.99, 63.66
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Erbin / Densin-180-like protein / Erbb2-interacting protein / Protein LAP2


Mass: 10273.659 Da / Num. of mol.: 2 / Mutation: S1294R, S1296A, V1351I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN, ERBB2IP, KIAA1225, LAP2 / Plasmid: pHH0103
Details (production host): 6His and GST at N-terminus followed by TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RT1
#2: Protein/peptide peptide /


Mass: 916.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 14% PEG3350,200 mM MgCl2, 100 mM MES 6.0. Cryoprotected with this condition plus 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→37.14 Å / Num. obs: 12494 / % possible obs: 91.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 18.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4051 / CC1/2: 0.941 / % possible all: 73.2

-
Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swiss-Modeller model of this PDZ

Resolution: 1.89→37.14 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.237 1250 10.01 %
Rwork0.178 --
obs0.184 12486 91.1 %
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.89→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 8 134 1700
LS refinement shellResolution: 1.886→1.9615 Å
RfactorNum. reflection% reflection
Rfree0.369 127 -
Rwork0.2787 1145 -
obs--83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31481.1276-0.22285.5477-2.43452.7709-0.02910.1055-0.077-0.07930.2354-0.1985-0.0718-0.1529-0.23710.3330.0198-0.07130.2331-0.01640.15376.753913.13482.706
24.7182-0.4528-5.4972.21420.36777.66470.1404-1.558-0.74110.36830.23580.24210.44420.2041-0.33770.2369-0.0465-0.01040.34350.06630.21012.674.804816.971
37.810.76680.34815.22280.53425.15940.02910.0011-0.3789-0.0653-0.018-0.08370.11260.13150.02930.18680.0384-0.02380.13510.0030.131415.87464.7488.8335
42.5294-2.02390.77775.91212.36548.78410.17810.04140.0613-0.0168-0.2144-0.5795-0.71010.59380.08140.2769-0.0448-0.02490.18030.05570.211615.059617.470811.3253
54.7801-1.2036-1.94982.1376-1.33752.76660.5464-0.9673-0.0770.2501-0.15080.0237-0.55160.739-0.30410.3908-0.0194-0.05340.2803-0.05250.182414.067912.356919.6587
66.22261.7229-0.21435.6061-2.14878.45250.31020.17320.4865-0.07540.1409-0.0204-0.4005-0.4942-0.26320.20840.0558-0.08620.22130.00080.1557.710912.38337.7739
76.15020.91890.26141.8346-3.06055.9061-0.1260.0450.22380.1725-0.081-0.4744-0.050.11360.20470.27210.0568-0.01220.1682-0.06740.16626.4716-8.9527-5.2723
87.99990.0115-0.73925.78180.09664.29110.05090.39130.2283-0.19680.05440.35180.0598-0.0806-0.08610.24830.0328-0.06220.15470.02050.148216.8788-9.6031-12.8191
91.09281.01730.5585.56730.55843.87750.13640.05610.13580.48280.09270.6616-0.1139-0.1671-0.1580.35510.0850.06230.1685-0.01760.270114.995-4.795-1.8368
103.6225-0.3108-0.50756.8155-0.69634.4510.2864-0.2353-0.15031.0047-0.1277-0.55130.0663-0.1284-0.20360.18120.0405-0.04170.2557-0.01440.140623.7888-9.7629-3.5765
115.224-2.6035-1.33261.48890.86660.8778-0.1675-0.5843-0.70760.5338-0.2063-0.31150.21730.28110.08790.19430.0099-0.12650.28020.14180.397517.77272.343216.5936
121.6227-1.9828-2.04372.38372.4282.95560.28240.47760.3072-0.34550.23240.4659-0.4469-1.027-0.4380.2348-0.0056-0.07190.36770.16580.37514.3472-2.2953-15.2749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 79 )
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 92 )
11X-RAY DIFFRACTION11chain 'C' and (resid -4 through 2 )
12X-RAY DIFFRACTION12chain 'D' and (resid -4 through 2 )

+
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