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- PDB-4x83: Crystal structure of Dscam1 isoform 7.44, N-terminal four Ig domains -

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Basic information

Entry
Database: PDB / ID: 4x83
TitleCrystal structure of Dscam1 isoform 7.44, N-terminal four Ig domains
ComponentsDown syndrome cell adhesion molecule, isoform 7.44
KeywordsCELL ADHESION / Ig fold
Function / homology
Function and homology information


DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon guidance receptor activity / axon extension involved in axon guidance / cell-cell adhesion mediator activity ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / detection of mechanical stimulus involved in sensory perception of touch / ventral cord development / dendrite self-avoidance / axon guidance receptor activity / axon extension involved in axon guidance / cell-cell adhesion mediator activity / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / neuron development / phagocytosis / antigen binding / axon guidance / central nervous system development / perikaryon / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell adhesion molecule Dscam1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsChen, Q. / Yu, Y. / Li, S.A. / Cheng, L.
CitationJournal: Sci Adv / Year: 2016
Title: Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition
Authors: Li, S.A. / Cheng, L. / Yu, Y. / Chen, Q.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Down syndrome cell adhesion molecule, isoform 7.44
B: Down syndrome cell adhesion molecule, isoform 7.44
C: Down syndrome cell adhesion molecule, isoform 7.44
D: Down syndrome cell adhesion molecule, isoform 7.44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,05513
Polymers172,6234
Non-polymers2,4329
Water26,2301456
1
A: Down syndrome cell adhesion molecule, isoform 7.44
B: Down syndrome cell adhesion molecule, isoform 7.44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6387
Polymers86,3112
Non-polymers1,3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-2 kcal/mol
Surface area37730 Å2
MethodPISA
2
C: Down syndrome cell adhesion molecule, isoform 7.44
D: Down syndrome cell adhesion molecule, isoform 7.44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4176
Polymers86,3112
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-5 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.734, 88.248, 94.310
Angle α, β, γ (deg.)98.18, 98.79, 90.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Down syndrome cell adhesion molecule, isoform 7.44


Mass: 43155.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0E9K9*PLUS
#2: 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.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 3 / 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1456 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium chloride 17%(w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.902→49.444 Å / Num. obs: 148198 / % possible obs: 93.55 % / Redundancy: 2.16 % / Net I/σ(I): 9.64

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DMK

3dmk


Resolution: 1.902→49.444 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1000 0.7 %
Rwork0.1934 --
obs0.1936 143198 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→49.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12041 0 155 1456 13652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812581
X-RAY DIFFRACTIONf_angle_d1.18917072
X-RAY DIFFRACTIONf_dihedral_angle_d14.1154655
X-RAY DIFFRACTIONf_chiral_restr0.0421950
X-RAY DIFFRACTIONf_plane_restr0.0052214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9016-2.00190.31421330.262418871X-RAY DIFFRACTION87
2.0019-2.12730.28261450.23720672X-RAY DIFFRACTION95
2.1273-2.29160.26951450.225920664X-RAY DIFFRACTION95
2.2916-2.52220.29131470.219120736X-RAY DIFFRACTION96
2.5222-2.88710.27941450.214220661X-RAY DIFFRACTION95
2.8871-3.63730.22331440.188920560X-RAY DIFFRACTION95
3.6373-49.46030.18231410.155520034X-RAY DIFFRACTION92

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