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- PDB-2v5m: Structural basis for Dscam isoform specificity -

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Basic information

Entry
Database: PDB / ID: 2v5m
TitleStructural basis for Dscam isoform specificity
ComponentsDSCAM
KeywordsCELL ADHESION / DOWN SYNDROME CELL ADHESION MOLECULE DSCAM / NEUROBIOLOGY SPL / IMMUNOGLOBULIN DOMAIN / MEMBRANE / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


DSCAM interactions / mushroom body development / detection of molecule of bacterial origin / 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 / mushroom body development / detection of molecule of bacterial origin / 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 / neuron projection / cell adhesion / axon / neuronal cell body / dendrite / 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 / 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 / MAD / Resolution: 1.95 Å
AuthorsMeijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Schmucker, D. / Wang, J.-H.
CitationJournal: Nature / Year: 2007
Title: Structural Basis of Dscam Isoform Specificity
Authors: Meijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Wang, J.-H. / Schmucker, D.
History
DepositionJul 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
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_special_symmetry / pdbx_validate_close_contact / 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 / _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_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSCAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8214
Polymers42,8811
Non-polymers9413
Water12,773709
1
A: DSCAM
hetero molecules

A: DSCAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6438
Polymers85,7612
Non-polymers1,8826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+2,y,-z1
Buried area4160 Å2
ΔGint-14.1 kcal/mol
Surface area44800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)99.172, 99.172, 163.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-2171-

HOH

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Components

#1: Protein DSCAM / DOWN SYNDROME CELL ADHESION MOLECULE DSCAM


Mass: 42880.582 Da / Num. of mol.: 1
Fragment: N-TERMINAL FOUR DOMAINS (D1, D2, D3 AND D4), RESIDUES 36-423
Source method: isolated from a genetically manipulated source
Details: ISOFORM 4.1/6.34 / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Organ: BRAIN / Variant: SPLICING VARIANT 4.1/6.34 / Plasmid: BACNBLUE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NBA1
#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.: 2
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE ...THE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE PROTEIN WHERE EXON 4 COVERING RESIDUES 102 TO 156 CONSISTS OF ISOFORM 1 AND EXON 6 COVERING RESIDUES 205 TO 245 CONSISTS OF ISOFORM 34.

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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: 4.6 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growDetails: 1.5 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 2005 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 271422 / % possible obs: 97.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.216 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3003 5 %RANDOM
Rwork0.169 ---
obs0.171 56543 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 62 709 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223280
X-RAY DIFFRACTIONr_bond_other_d0.0020.022279
X-RAY DIFFRACTIONr_angle_refined_deg2.6561.9844462
X-RAY DIFFRACTIONr_angle_other_deg1.5083.0015553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4515402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85523.974151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02415566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8521526
X-RAY DIFFRACTIONr_chiral_restr0.150.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023591
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02635
X-RAY DIFFRACTIONr_nbd_refined0.2940.2687
X-RAY DIFFRACTIONr_nbd_other0.2480.22507
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21526
X-RAY DIFFRACTIONr_nbtor_other0.1130.21870
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.2508
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.420.261
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2631.52537
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63123253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.46931470
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9594.51206
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 177 -
Rwork0.219 3844 -
obs--92.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75411.43-1.1996.4743-0.35712.643-0.0674-0.1516-0.07190.1774-0.04760.40690.0723-0.17720.1151-0.04190.05040.117-0.21160.0532-0.240779.26421.64431.237
20.9727-0.4095-0.57951.49970.41312.36520.02490.05450.0072-0.12350.02530.1285-0.07590.0816-0.0501-0.0726-0.01170.0092-0.30050.0218-0.265287.66138.98-3.598
31.55440.727-0.41082.0299-0.82722.140.0072-0.1009-0.1875-0.15740.01270.11640.23720.0244-0.02-0.05010.00110.0113-0.2981-0.0009-0.233590.13918.383-9.378
43.11030.4091-1.08726.7335-0.74316.0021-0.1578-0.1827-0.41120.6498-0.02550.38030.74730.06730.18320.17150.01570.2243-0.24080.0424-0.068879.206-1.52924.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A104 - 207
4X-RAY DIFFRACTION3A208 - 305
5X-RAY DIFFRACTION3A501 - 503
6X-RAY DIFFRACTION4A306 - 388

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