[English] 日本語
Yorodumi
- PDB-3dmk: Crystal structure of Down Syndrome Cell Adhesion Molecule (DSCAM)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dmk
TitleCrystal structure of Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
ComponentsDown Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
KeywordsCELL ADHESION / Ig Domains / Immunoglobulin domain
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 / 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
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Cell adhesion molecule Dscam1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.19 Å
AuthorsSawaya, M.R. / Wojtowicz, W.M. / Eisenberg, D. / Zipursky, S.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.
Authors: Sawaya, M.R. / Wojtowicz, W.M. / Andre, I. / Qian, B. / Wu, W. / Baker, D. / Eisenberg, D. / Zipursky, S.L.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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.end_auth_comp_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
B: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
C: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,86216
Polymers269,1893
Non-polymers4,67213
Water00
1
A: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
B: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,87713
Polymers179,4592
Non-polymers3,41711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-26.5 kcal/mol
Surface area73710 Å2
MethodPISA
2
C: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
hetero molecules

C: Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,9706
Polymers179,4592
Non-polymers2,5104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area4840 Å2
ΔGint-26.3 kcal/mol
Surface area68320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.460, 177.610, 434.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23C
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLYGLY2AA1 - 17236 - 207
211GLNGLNGLYGLY2BB1 - 17236 - 207
311GLNGLNGLYGLY2CC1 - 17236 - 207
121LYSLYSTHRTHR2AA178 - 204213 - 239
221LYSLYSTHRTHR2BB178 - 204213 - 239
321LYSLYSTHRTHR2CC178 - 204213 - 239
131PROPROLYSLYS2AA206 - 387241 - 422
231PROPROLYSLYS2BB206 - 387241 - 422
331PROPROLYSLYS2CC206 - 387241 - 422
141PROPROTYRTYR5AA173 - 177208 - 212
241PROPROTYRTYR5BB173 - 177208 - 212
341PROPROTYRTYR5CC173 - 177208 - 212
112PHEPHEASNASN2AA392 - 488427 - 523
212PHEPHEASNASN2BB392 - 488427 - 523
312PHEPHEASNASN2CC392 - 488427 - 523
122LEULEUASNASN2AA492 - 529527 - 564
222LEULEUASNASN2BB492 - 529527 - 564
322LEULEUASNASN2CC492 - 529527 - 564
132GLNGLNGLUGLU2AA538 - 577573 - 612
232GLNGLNGLUGLU2BB538 - 577573 - 612
332GLNGLNGLUGLU2CC538 - 577573 - 612
113VALVALARGARG2BB582 - 585617 - 620
213VALVALARGARG2CC582 - 585617 - 620
123GLNGLNLEULEU2BB597 - 674632 - 709
223GLNGLNLEULEU2CC597 - 674632 - 709
114VALVALLEULEU2AA582 - 674617 - 709
214VALVALLEULEU2BB582 - 674617 - 709

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein Down Syndrome Cell Adhesion Molecule (DSCAM) isoform 1.30.30, N-terminal eight Ig domains


Mass: 89729.719 Da / Num. of mol.: 3 / Fragment: N-terminal Eight Ig Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q0E9I4*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: 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: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY
Sequence detailsTHE SEQUENCE REPORTED BY AUTHORS IS OF ISOFORM 1.30.30

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.28M Ammonium sulfate, 0.2M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 4.19→90 Å / Num. all: 34106 / Num. obs: 34106 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.103 / Net I/σ(I): 9
Reflection shellResolution: 4.19→4.46 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.462 / Num. unique all: 5605 / Χ2: 1.043 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V5M

2v5m


Resolution: 4.19→12 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.744 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.768 / SU B: 144.897 / SU ML: 0.899 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1618 5 %RANDOM
Rwork0.28 ---
obs0.282 32525 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 108.15 Å2 / Biso mean: 54.028 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---2.07 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 4.19→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16431 0 309 0 16740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02918786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211630
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.97923302
X-RAY DIFFRACTIONr_angle_other_deg0.7783.00328278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5552123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37824.278741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.899152802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.02115107
X-RAY DIFFRACTIONr_chiral_restr0.0570.22646
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023298
X-RAY DIFFRACTIONr_mcbond_it1.042211973
X-RAY DIFFRACTIONr_mcbond_other0.12824304
X-RAY DIFFRACTIONr_mcangle_it1.438317165
X-RAY DIFFRACTIONr_scbond_it0.75726695
X-RAY DIFFRACTIONr_scangle_it1.27736137
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2238TIGHT POSITIONAL0.010.05
1B2238TIGHT POSITIONAL0.010
1C2238TIGHT POSITIONAL0.010
1A2834MEDIUM POSITIONAL0.010.5
1B2834MEDIUM POSITIONAL0.010
1C2834MEDIUM POSITIONAL0.010
1A40LOOSE POSITIONAL0.035
1B40LOOSE POSITIONAL0.020.12
1C40LOOSE POSITIONAL0.040
1A2238TIGHT THERMAL8.2850
1B2238TIGHT THERMAL5.980.02
1C2238TIGHT THERMAL6.40
1A2834MEDIUM THERMAL8.0460
1B2834MEDIUM THERMAL5.910.02
1C2834MEDIUM THERMAL6.290
1A40LOOSE THERMAL6.5980
1B40LOOSE THERMAL1.362
1C40LOOSE THERMAL5.610.05
2A1026TIGHT POSITIONAL0.020.05
2B1026TIGHT POSITIONAL0.010
2C1026TIGHT POSITIONAL0.020
2A1246MEDIUM POSITIONAL0.020.5
2B1246MEDIUM POSITIONAL0.010
2C1246MEDIUM POSITIONAL0.020
2A1026TIGHT THERMAL9.2250
2B1026TIGHT THERMAL5.740.05
2C1026TIGHT THERMAL6.280
2A1246MEDIUM THERMAL8.9660
2B1246MEDIUM THERMAL5.730.05
2C1246MEDIUM THERMAL6.470
3B479TIGHT POSITIONAL0.010.05
3C548MEDIUM POSITIONAL0.010.5
3B479TIGHT THERMAL9.7750
3C548MEDIUM THERMAL9.6160
4A542TIGHT POSITIONAL0.010.05
4A630MEDIUM POSITIONAL0.010.5
4B542TIGHT THERMAL5.0650
4B630MEDIUM THERMAL5.0960
LS refinement shellResolution: 4.19→4.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 97 -
Rwork0.291 1897 -
all-1994 -
obs--90.93 %
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)
119.9261-15.35588.633823.1604-8.35829.99870.57051.3249-0.3999-2.6417-0.60651.3857-0.5755-1.34470.0361-0.01230.3494-0.61510.287-0.3887-0.7947-56.85521.51661.851
29.93130.34973.03887.03444.562622.26320.3368-0.2883-0.9370.3348-1.02690.44380.7232-0.61870.6901-1.0905-0.08050.0278-0.6941-0.1567-0.5346-44.87813.0199.115
310.2777-0.56956.88698.867-2.01759.806-0.03620.130.93520.0812-0.6237-0.0356-0.88890.07880.6598-1.0830.03370.2595-0.3961-0.5312-0.6863-48.5534.47101.902
43.35533.7827-3.87420.77080.572616.45651.03730.92932.094-5.0396-0.03841.8776-1.6904-1.5189-0.99881.02331.0154-0.45260.59320.08970.4036-64.86343.95964.904
59.9198-0.2694-3.27321.24860.55681.25640.3765-0.8458-2.9772-1.94871.48250.3267-2.7192-1.3695-1.85893.91090.4256-1.0093.20470.6072.754-74.6469.27834.597
65.32099.44290.855616.75791.51830.13760.12681.12-0.3223-1.35590.47380.0966-1.3274-0.1665-0.60073.75081.00450.4353.7885-0.1241-0.6488-50.26477.20440.209
78.27754.285-2.844913.5003-9.828616.83340.48252.0312-0.2072-2.14460.31830.6160.48520.9143-0.80080.77130.734-0.12060.4142-0.6254-1.4708-59.74973.11781.757
85.38290.08721.470621.517-5.581617.49890.03140.1223-1.3250.34360.32060.60310.9923-0.0024-0.352-0.83560.11550.0225-0.7817-0.4353-0.3352-59.45947.52119.09
94.98474.50761.395431.23496.28173.27170.8996-0.74850.3831.8367-0.5228-0.05670.6821-0.2539-0.3768-0.951-0.23080.313-0.1654-0.3682-0.9559-19.10341.115124.057
105.90132.02112.84435.14642.581110.5260.4223-0.4328-0.5940.0849-0.2093-0.10920.71420.038-0.213-1.17710.05930.0668-0.9671-0.061-0.773-22.40117.94691.539
117.10293.53095.937616.30634.486810.1718-0.4227-0.02850.9759-0.6137-0.24911.0912-1.3424-0.45230.6718-0.84350.17380.1939-0.8788-0.0031-0.7113-29.12236.63883.022
128.46790.036-0.465421.63089.35718.26980.4295-0.06230.7993-0.2294-0.51751.2464-0.23640.22960.0881-0.8043-0.03110.2824-0.6741-0.267-0.2599-22.93762.752114.336
1321.21175.7523-6.07314.6569-0.45196.84570.78610.23140.05060.1202-0.4076-0.7719-0.0770.0688-0.3786-0.90670.0444-0.0758-1.16970.048-1.0833-37.28386.426139.664
145.20690.786-2.24427.25033.770519.4058-0.22820.8571-0.5916-0.24620.0221-0.34430.36140.68260.2061-1.2414-0.0423-0.0124-0.9856-0.1565-0.9105-54.97170.428128.398
1512.22563.4159-2.667514.08462.258219.38760.88341.99810.1446-2.1814-0.45-1.2132-1.96380.6051-0.43350.32150.4410.56470.47170.1326-0.8684-43.35882.33988.903
1613.53975.5489-4.338214.6584-0.26661.57441.4866-2.99850.9147-0.9657-0.37562.2688-1.34040.0238-1.11113.27860.0825-0.81690.17830.72120.8195-22.860.2930.38
1710.7150.5575-13.98013.156-0.334918.28941.4665-5.2061.0339-0.01230.50990.856-0.018111.0929-1.97632.47650.1207-0.34256.3391-0.41090.2059-11.21377.922-4.309
1817.20273.4854-5.47215.87493.140318.06590.76231.43570.2143-0.09840.6555-0.97490.25970.9663-1.41773.21320.008-0.5765-0.18940.40850.258-9.30957.151-9.968
194.19014.2356-9.366922.267-13.52821.85570.09120.2107-0.7979-1.89110.25380.6154-2.2024-0.9548-0.34491.6553-0.1606-1.23010.29650.53140.5706-24.1638.03523.417
2019.4642-0.51699.9447.0693-4.275111.8805-0.25361.21320.3002-1.18380.69871.750.0531-0.6273-0.4452-0.32130.0292-0.2014-0.80890.1855-0.9118-17.88411.53350.86
2111.37844.1408-1.654510.9506-11.350433.8036-0.60982.44651.7587-1.4460.1123-0.7376-1.24030.74460.4976-0.11730.05160.1044-0.43150.6138-0.88485.60922.5443.936
2216.88782.26678.30075.43651.124329.1162-0.2163-1.5205-1.01670.38810.64460.916-0.2249-1.7273-0.42830.99090.0345-0.0836-0.10340.3829-1.5505-8.98923.3834.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 10436 - 139
2X-RAY DIFFRACTION1AD782 - 783
3X-RAY DIFFRACTION2AA105 - 209140 - 244
4X-RAY DIFFRACTION3AA210 - 305245 - 340
5X-RAY DIFFRACTION3AE784 - 785
6X-RAY DIFFRACTION4AA306 - 388341 - 423
7X-RAY DIFFRACTION5AA389 - 489424 - 524
8X-RAY DIFFRACTION6AA490 - 581525 - 616
9X-RAY DIFFRACTION7AA582 - 680617 - 715
10X-RAY DIFFRACTION8AA681 - 775716 - 810
11X-RAY DIFFRACTION9BB1 - 10436 - 139
12X-RAY DIFFRACTION9BF782 - 783
13X-RAY DIFFRACTION10BB105 - 209140 - 244
14X-RAY DIFFRACTION11BB210 - 305245 - 340
15X-RAY DIFFRACTION11BK790 - 791
16X-RAY DIFFRACTION12BB306 - 388341 - 423
17X-RAY DIFFRACTION13BB389 - 489424 - 524
18X-RAY DIFFRACTION13BI787 - 789
19X-RAY DIFFRACTION14BB490 - 581525 - 616
20X-RAY DIFFRACTION14BH784 - 786
21X-RAY DIFFRACTION15BB582 - 676617 - 711
22X-RAY DIFFRACTION16CC1 - 10436 - 139
23X-RAY DIFFRACTION17CC105 - 209140 - 244
24X-RAY DIFFRACTION18CC210 - 305245 - 340
25X-RAY DIFFRACTION19CC306 - 388341 - 423
26X-RAY DIFFRACTION20CC389 - 489424 - 524
27X-RAY DIFFRACTION20CG782 - 784
28X-RAY DIFFRACTION21CC490 - 581525 - 616
29X-RAY DIFFRACTION21CJ785 - 787
30X-RAY DIFFRACTION22CC582 - 676617 - 711

+
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