[English] 日本語
Yorodumi
- PDB-3bin: Structure of the DAL-1 and TSLC1 (372-383) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bin
TitleStructure of the DAL-1 and TSLC1 (372-383) complex
Components
  • Band 4.1-like protein 3
  • Cell adhesion molecule 1
KeywordsCELL ADHESION / FERM domain / DAL-1 / TSLC1 / Actin-binding / Cytoskeleton / Phosphoprotein / Structural protein / Anti-oncogene / Apoptosis / Cell cycle / Developmental protein / Differentiation / Glycoprotein / Immune response / Immunoglobulin domain / Membrane / Spermatogenesis / Transmembrane
Function / homology
Function and homology information


negative regulation of ERBB4 signaling pathway / detection of stimulus / cell recognition / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance ...negative regulation of ERBB4 signaling pathway / detection of stimulus / cell recognition / susceptibility to natural killer cell mediated cytotoxicity / Nectin/Necl trans heterodimerization / protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / positive regulation of natural killer cell mediated cytotoxicity / paranode region of axon / cortical cytoskeleton organization / juxtaparanode region of axon / Adherens junctions interactions / actomyosin structure organization / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cortical actin cytoskeleton organization / immune system process / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / neuron projection morphogenesis / negative regulation of protein phosphorylation / liver development / positive regulation of cytokine production / protein localization to plasma membrane / PDZ domain binding / structural constituent of cytoskeleton / cell-cell junction / cell junction / actin binding / regulation of cell shape / spermatogenesis / basolateral plasma membrane / postsynaptic density / cell differentiation / cytoskeleton / neuron projection / signaling receptor binding / apoptotic process / synapse / dendrite / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) ...Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain / FERM superfamily, second domain / Immunoglobulin domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell adhesion molecule 1 / Band 4.1-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsBusam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. ...Busam, R.D. / Arrowsmith, C.H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Berglund, H. / Persson, C. / Hallberg, B.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of tumor suppressor in lung cancer 1 (TSLC1) binding to differentially expressed in adenocarcinoma of the lung (DAL-1/4.1B)
Authors: Busam, R.D. / Thorsell, A.-G. / Flores, A. / Hammarstrom, M. / Persson, C. / Obrink, B. / Hallberg, B.M.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Band 4.1-like protein 3
B: Cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)34,4432
Polymers34,4432
Non-polymers00
Water2,594144
1
A: Band 4.1-like protein 3


Theoretical massNumber of molelcules
Total (without water)33,0221
Polymers33,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell adhesion molecule 1


  • defined by author
  • 1.42 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,4221
Polymers1,4221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.000, 135.000, 50.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Band 4.1-like protein 3 / 4.1B / Differentially expressed in adenocarcinoma of the lung protein 1 / DAL-1


Mass: 33021.812 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41L3, DAL1, KIAA0987 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRare2 / References: UniProt: Q9Y2J2
#2: Protein/peptide Cell adhesion molecule 1 / Immunoglobulin superfamily member 4 / Nectin-like protein 2 / NECL-2 / Tumor suppressor in lung ...Immunoglobulin superfamily member 4 / Nectin-like protein 2 / NECL-2 / Tumor suppressor in lung cancer 1 / TSLC-1 / Synaptic cell adhesion molecule / Spermatogenic immunoglobulin superfamily / SgIGSF


Mass: 1421.559 Da / Num. of mol.: 1
Fragment: Peptide from cytoplasmic domain, UNP residues 400-411
Source method: obtained synthetically / Details: Peptide synthetic / References: UniProt: Q9BY67
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% ETOH, 0.1M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.03992 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03992 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 23666 / Num. obs: 23489 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.65 % / Rsym value: 0.047 / Net I/σ(I): 18.89
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.75 % / Mean I/σ(I) obs: 2.95 / Num. unique all: 1748 / Rsym value: 0.417 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.911 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1131 4.9 %RANDOM
Rwork0.179 ---
all0.181 23666 --
obs0.181 23120 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.697 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 0 144 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222497
X-RAY DIFFRACTIONr_bond_other_d0.0020.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.953375
X-RAY DIFFRACTIONr_angle_other_deg0.99834251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79923.125128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7151520
X-RAY DIFFRACTIONr_chiral_restr0.1080.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_nbd_refined0.2090.2487
X-RAY DIFFRACTIONr_nbd_other0.2070.21774
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21141
X-RAY DIFFRACTIONr_nbtor_other0.0930.21318
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.216
X-RAY DIFFRACTIONr_mcbond_it1.0071.51904
X-RAY DIFFRACTIONr_mcbond_other0.2131.5593
X-RAY DIFFRACTIONr_mcangle_it1.25222383
X-RAY DIFFRACTIONr_scbond_it2.25531212
X-RAY DIFFRACTIONr_scangle_it3.074.5992
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 75 -
Rwork0.259 1649 -
all-1724 -
obs--100 %
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)
16.15042.44543.1644.31931.70692.9907-0.18390.14320.2839-0.1656-0.0154-0.135-0.17160.25380.1993-0.21220.04790.0199-0.17050.0034-0.281462.7748.654-7.739
26.77141.2362.00532.56920.73132.1302-0.0689-0.57120.31510.0877-0.10220.1852-0.1573-0.23560.1712-0.20670.08050.0073-0.1614-0.0246-0.226655.31150.031-2.642
37.23933.36412.99818.56754.00562.2160.2691-1.4547-0.2520.4688-0.22230.63160.1356-0.3481-0.0468-0.0645-0.00020.09930.24370.12910.00739.14836.9452.395
42.2946-1.12786.0295.51120.540218.3171-0.008-0.4499-1.85380.42260.06120.74174.0298-0.113-0.05330.5708-0.0054-0.0010.06090.11230.616238.32620.076-6.602
53.24350.1356-4.216532.437118.389818.28630.7723-0.7452-1.10242.2095-0.6511-0.52912.3784-0.7279-0.12120.466-0.0362-0.12340.44510.35850.362142.62926.6175.195
64.9716-0.76260.08059.4596-1.84339.34030.1423-0.6913-0.99620.5204-0.18711.03570.8467-0.20050.0448-0.0963-0.04810.06090.07640.12330.259635.0629.263-3.89
70.89952.08211.019410.97474.40491.8348-0.4043-0.5825-0.04540.6755-0.11760.79390.259-0.89790.522-0.12170.07980.15910.449-0.18820.068141.26154.5157.046
811.6363-1.24380.681712.5414-0.4866.1828-0.492-0.430.07140.14740.6560.57680.4542-0.4339-0.164-0.06610.15520.09540.0916-0.18480.014841.58165.1978.073
914.6996-7.1970.78025.0205-0.70050.8562-0.1992-0.30011.1050.26610.4614-0.4606-0.14910.3051-0.2622-0.04390.04680.0652-0.007-0.11960.05441.72172.4629.652
1014.54541.889112.799510.23857.704827.0294-0.13180.45720.5908-0.7427-0.0925-0.0018-0.5720.7320.2244-0.06270.14740.0567-0.1054-0.0482-0.037350.28563.2090.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA108 - 1561 - 49
2X-RAY DIFFRACTION2AA157 - 21250 - 105
3X-RAY DIFFRACTION3AA213 - 236106 - 129
4X-RAY DIFFRACTION4AA237 - 243130 - 136
5X-RAY DIFFRACTION5AA244 - 262137 - 155
6X-RAY DIFFRACTION6AA263 - 283156 - 176
7X-RAY DIFFRACTION7AA284 - 321177 - 214
8X-RAY DIFFRACTION8AA322 - 344215 - 237
9X-RAY DIFFRACTION9AA345 - 369238 - 262
10X-RAY DIFFRACTION10AA370 - 390263 - 283

+
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://pdbjlvh1.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