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- PDB-4xb7: Crystal structure of Dscam1 isoform 4.4, N-terminal four Ig domains -

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Basic information

Entry
Database: PDB / ID: 4xb7
TitleCrystal structure of Dscam1 isoform 4.4, N-terminal four Ig domains
ComponentsDown syndrome cell adhesion molecule, isoform 4.4
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 / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / peripheral nervous system development ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / central nervous system morphogenesis / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / phagocytosis / neuron development / antigen binding / axon guidance / perikaryon / cell adhesion / neuron projection / axon / neuronal cell body / dendrite / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / DSCAM/DSCAML C-terminal Fn3-like domain / 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 ...: / DSCAM/DSCAML C-terminal Fn3-like domain / 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 / Immunoglobulin-like fold / Immunoglobulins / 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: 4.004 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 16, 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: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _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 30, 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 4.4
B: Down syndrome cell adhesion molecule, isoform 4.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9116
Polymers87,7272
Non-polymers2,1844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint18 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.212, 100.212, 351.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Down syndrome cell adhesion molecule, isoform 4.4


Mass: 43863.414 Da / Num. of mol.: 2 / Fragment: N-terminal four Ig domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0E9L0*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 1
Source method: isolated from a genetically manipulated source
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
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: 5.03 Å3/Da / Density % sol: 75.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.5M Magnesium Chloride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4→50.106 Å / Num. obs: 15793 / % possible obs: 99.9 % / Redundancy: 9.6 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5M

2v5m


Resolution: 4.004→50.106 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 791 5.01 %
Rwork0.2236 --
obs0.2252 15793 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.004→50.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 145 0 6257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046400
X-RAY DIFFRACTIONf_angle_d0.8678686
X-RAY DIFFRACTIONf_dihedral_angle_d13.4262390
X-RAY DIFFRACTIONf_chiral_restr0.038997
X-RAY DIFFRACTIONf_plane_restr0.0041124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0044-4.25520.29231250.24942312X-RAY DIFFRACTION95
4.2552-4.58350.25591170.21162482X-RAY DIFFRACTION100
4.5835-5.04440.25321340.20842470X-RAY DIFFRACTION100
5.0444-5.77340.24481410.21262477X-RAY DIFFRACTION100
5.7734-7.27040.24581380.2452548X-RAY DIFFRACTION100
7.2704-50.10990.25681360.22212713X-RAY DIFFRACTION100

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