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- PDB-7lir: Structure of the invertebrate ALK GRD -

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Basic information

Entry
Database: PDB / ID: 7lir
TitleStructure of the invertebrate ALK GRD
ComponentsALK tyrosine kinase receptor homolog scd-2
KeywordsSIGNALING PROTEIN / ALK / anaplastic lymphoma kinase / GRD / glycine rich domain / Pole / poly-glycine extension / PXL / poly-glycine extension loops / neuroblastoma / cancer / receptor / kinase / oncogene / AUG / augmentor / ALKAL / ALK and LTK activating ligand / FAM150
Function / homology
Function and homology information


dauer larval development / sensory processing / sensory perception of chemical stimulus / regulation of neuron differentiation / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / chemotaxis / ATP binding / plasma membrane
Similarity search - Function
Glycine rich protein / MAM domain / MAM domain profile. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...Glycine rich protein / MAM domain / MAM domain profile. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ALK tyrosine kinase receptor homolog scd-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsStayrook, S. / Li, T. / Klein, D.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K22 CA215821 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA248532 United States
CitationJournal: Nature / Year: 2021
Title: Structural basis for ligand reception by anaplastic lymphoma kinase.
Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / ...Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / Alvarado, D. / Lemmon, M.A. / Schlessinger, J. / Klein, D.E.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALK tyrosine kinase receptor homolog scd-2
B: ALK tyrosine kinase receptor homolog scd-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45715
Polymers76,6092
Non-polymers4,84813
Water3,045169
1
A: ALK tyrosine kinase receptor homolog scd-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7547
Polymers38,3041
Non-polymers2,4496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALK tyrosine kinase receptor homolog scd-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7038
Polymers38,3041
Non-polymers2,3997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.339, 224.339, 114.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALK tyrosine kinase receptor homolog scd-2 / Suppressor of constitutive dauer formation protein 2


Mass: 38304.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: scd-2, T10H9.2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O76411, receptor protein-tyrosine kinase

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Sugars , 6 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 174 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.5 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.84 M (NH4)2SO4, Bicine pH 9.0, 28 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2018 / Details: undulator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→112.42 Å / Num. obs: 44990 / % possible obs: 99.9 % / Redundancy: 26.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.04 / Rrim(I) all: 0.209 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1 / % possible all: 99.3

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.6-2.726.68.31812293546170.4251.6328.4790.5
9.72-50.1823.50.058224949590.9990.0120.0658.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20200417data reduction
SCALA0.7.4data scaling
SHELXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.6→50.18 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.656 / SU ML: 0.247 / SU R Cruickshank DPI: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 2175 4.8 %RANDOM
Rwork0.2233 ---
obs0.2255 42770 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 240.66 Å2 / Biso mean: 82.098 Å2 / Biso min: 37.66 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å2-0 Å20 Å2
2--2.24 Å2-0 Å2
3----4.47 Å2
Refinement stepCycle: final / Resolution: 2.6→50.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 315 169 5660
Biso mean--138.44 75.44 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135644
X-RAY DIFFRACTIONr_bond_other_d0.0050.0184837
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.7257631
X-RAY DIFFRACTIONr_angle_other_deg1.4021.65611241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5935680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93622.795297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8815793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7161533
X-RAY DIFFRACTIONr_chiral_restr0.0650.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021286
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 155 -
Rwork0.401 3105 -
all-3260 -
obs--99.88 %

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