[English] 日本語
Yorodumi
- PDB-2v5s: Structural basis for Dscam isoform specificity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v5s
TitleStructural basis for Dscam isoform specificity
ComponentsDSCAM
KeywordsCELL ADHESION / DOWN SYNDROME / IMMUNOGLOBULIN DOMAIN / MEMBRANE / DEVELOPMENTAL PROTEIN
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: 2.3 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 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / database_PDB_caveat / 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_validate_chiral / 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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 2.1Dec 13, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DSCAM
B: DSCAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8226
Polymers87,1252
Non-polymers1,6984
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-20.1 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.770, 166.842, 125.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 1 - 388 / Label seq-ID: 7 - 394

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.99985, -0.00253, 0.01723), (-0.00245, -0.99999, -0.00445), (0.01724, 0.00441, -0.99984)
Vector: -0.62316, -39.72151, 62.22053)

-
Components

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


Mass: 43562.273 Da / Num. of mol.: 2
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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 1.5 M AMMONIUM SULPHATE 0.1 M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 22250 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5M

2v5m


Resolution: 2.3→19.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.095 / SU ML: 0.24 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2254 5 %RANDOM
Rwork0.227 ---
obs0.23 42443 95.6 %-
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: 54.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6077 0 112 246 6435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226539
X-RAY DIFFRACTIONr_bond_other_d0.0010.024532
X-RAY DIFFRACTIONr_angle_refined_deg2.4921.9838899
X-RAY DIFFRACTIONr_angle_other_deg1.4033.00111046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.245800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83124.04302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.691151133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3841550
X-RAY DIFFRACTIONr_chiral_restr0.1440.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021269
X-RAY DIFFRACTIONr_nbd_refined0.2630.21304
X-RAY DIFFRACTIONr_nbd_other0.2350.24797
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22970
X-RAY DIFFRACTIONr_nbtor_other0.1020.23846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3360.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.55034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58226470
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.69632969
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0264.52424
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2284medium positional0.180.5
3012loose positional0.445
2284medium thermal0.792
3012loose thermal1.4810
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 154
Rwork0.346 2959
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)
112.5601-3.02475.51312.8088-1.58723.473-0.0580.62260.5799-0.34960.03710.13690.109-0.08030.02080.0156-0.06270.0135-0.07960.1865-0.013621.28410.37210.258
21.6266-0.0334-0.03572.495-1.13441.7432-0.03760.1035-0.18980.02490.0429-0.033-0.0270.023-0.0054-0.146-0.0289-0.023-0.1655-0.0189-0.314539.33-23.82620.163
32.669-2.20151.47165.1332-2.28113.7898-0.1186-0.0628-0.25620.00850.39660.8575-0.0374-0.5663-0.278-0.12-0.0584-0.0036-0.07830.1180.012118.462-29.73122.547
48.4169-2.1898-0.08686.1577-1.4584.8127-0.0904-0.08890.64570.2784-0.4007-0.0979-0.1862-0.0090.491-0.0849-0.0443-0.00410.04540.1362-0.0958-1.7734.0210.883
511.24454.2117-6.20152.8922-1.66023.75420.1748-0.545-0.45590.4392-0.1541-0.0521-0.1522-0.1272-0.02080.02690.0435-0.01430.01220.27420.04919.699-51.04253.077
61.735-0.33330.03162.617-1.28631.5509-0.0555-0.17180.0313-0.00870.0565-0.015-0.0756-0.0131-0.001-0.13910.02870.0019-0.1557-0.003-0.287739.194-16.06642.646
73.21481.2585-0.95283.2498-1.33212.7886-0.1374-0.04550.0316-0.04170.16960.32850.034-0.3751-0.0322-0.0830.07470.0248-0.09060.0192-0.188918.451-10.11939.971
84.81414.9138-1.332210.089-2.66723.9086-0.0057-0.08270.0352-0.0659-0.14711.03090.1538-0.16740.1528-0.02720.09990.1470.09260.25770.5298-2.015-43.98251.314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION1A1389 - 1390
3X-RAY DIFFRACTION2A104 - 208
4X-RAY DIFFRACTION3A209 - 305
5X-RAY DIFFRACTION3A1391 - 1392
6X-RAY DIFFRACTION4A306 - 388
7X-RAY DIFFRACTION5B-5 - 103
8X-RAY DIFFRACTION5B1389 - 1390
9X-RAY DIFFRACTION6B104 - 208
10X-RAY DIFFRACTION7B209 - 305
11X-RAY DIFFRACTION7B1391 - 1392
12X-RAY DIFFRACTION8B306 - 388

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more