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- PDB-3bin: Structure of the DAL-1 and TSLC1 (372-383) complex -

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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


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 / myelin maintenance / protein localization to juxtaparanode region of axon / positive regulation of natural killer cell mediated cytotoxicity ...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 / myelin maintenance / protein localization to juxtaparanode region of axon / positive regulation of natural killer cell mediated cytotoxicity / paranode region of axon / actomyosin structure organization / Adherens junctions interactions / cortical cytoskeleton organization / juxtaparanode region of axon / immune system process / Neurexins and neuroligins / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cortical actin cytoskeleton organization / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / neuron projection morphogenesis / protein localization to plasma membrane / PDZ domain binding / regulation of cell growth / positive regulation of cytokine production / structural constituent of cytoskeleton / cell-cell junction / cell junction / spermatogenesis / actin binding / regulation of cell shape / basolateral plasma membrane / cytoskeleton / multicellular organism development / cell differentiation / synapse / signaling receptor binding / apoptotic process / viral process / protein homodimerization activity / integral component of membrane / 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) / putative band 4.1 homologues' binding motif / Neurexin/syndecan/glycophorin C / 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) / putative band 4.1 homologues' binding motif / Neurexin/syndecan/glycophorin C / 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, N-terminal / FERM C-terminal PH-like domain / FERM, C-terminal PH-like domain / 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 / FERM central domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Immunoglobulin C-2 Type / Immunoglobulin subtype 2 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Immunoglobulin / Immunoglobulin subtype / Ubiquitin-like domain superfamily / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Roll / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
γ
α
β
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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1

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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

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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

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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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

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