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- PDB-4x9h: Crystal structure of Dscam1 isoform 8.4, N-terminal four Ig domains -

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Basic information

Entry
Database: PDB / ID: 4x9h
TitleCrystal structure of Dscam1 isoform 8.4, N-terminal four Ig domains
ComponentsDown syndrome cell adhesion molecule, isoform AP
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: 2.95 Å
AuthorsChen, Q.
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 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
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 / 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_struct_assembly_gen.asym_id_list / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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 AP
B: Down syndrome cell adhesion molecule, isoform AP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9616
Polymers88,0212
Non-polymers1,9404
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint14 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.222, 60.950, 92.351
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Down syndrome cell adhesion molecule, isoform AP / Down syndrome cell adhesion molecule isoform 8.4


Mass: 44010.734 Da / Num. of mol.: 2 / Fragment: UNP residues 34-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam1, Dscam, CG17800, Dmel_CG17800 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0E9L0
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH6.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2014
RadiationMonochromator: SiIII double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 22498 / % possible obs: 97.2 % / Redundancy: 2.7 % / Net I/σ(I): 14.1

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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: 2.95→47.519 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3235 1149 5.12 %
Rwork0.2717 --
obs0.2744 22450 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→47.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 128 3 6218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046373
X-RAY DIFFRACTIONf_angle_d1.0078648
X-RAY DIFFRACTIONf_dihedral_angle_d15.3942388
X-RAY DIFFRACTIONf_chiral_restr0.036992
X-RAY DIFFRACTIONf_plane_restr0.0041112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9503-3.08450.39331550.36982573X-RAY DIFFRACTION97
3.0845-3.24710.38991460.34572646X-RAY DIFFRACTION100
3.2471-3.45050.40581250.32712668X-RAY DIFFRACTION100
3.4505-3.71680.37231490.32222655X-RAY DIFFRACTION100
3.7168-4.09070.38731280.2922683X-RAY DIFFRACTION100
4.0907-4.68210.30211680.25572653X-RAY DIFFRACTION100
4.6821-5.89730.28071580.24062672X-RAY DIFFRACTION100
5.8973-47.52530.27661200.23252751X-RAY DIFFRACTION98

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