[English] 日本語
Yorodumi
- PDB-6nrq: Crystal structure of Dpr10 IG1 bound to DIP-alpha IG1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nrq
TitleCrystal structure of Dpr10 IG1 bound to DIP-alpha IG1
Components
  • Defective proboscis extension response 10, isoform A
  • Dpr-interacting protein alpha, isoform A
KeywordsCELL ADHESION / Immunoglobulin superfamily / Glycoprotein / Neuronal / Cell surface receptor
Function / homology
Function and homology information


Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / neuron projection membrane / Glycosaminoglycan-protein linkage region biosynthesis / sensory perception of chemical stimulus / synapse organization ...Degradation of the extracellular matrix / Non-integrin membrane-ECM interactions / ECM proteoglycans / HS-GAG biosynthesis / HS-GAG degradation / Integrin cell surface interactions / neuron projection membrane / Glycosaminoglycan-protein linkage region biosynthesis / sensory perception of chemical stimulus / synapse organization / neuron projection / plasma membrane
Similarity search - Function
Zwei Ig domain protein zig-8 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Zwei Ig domain protein zig-8 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Defective proboscis extension response 10, isoform A / Dpr-interacting protein alpha, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCheng, S. / Park, Y.J. / Kurleto, J.D. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS097161 United States
CitationJournal: Elife / Year: 2019
Title: Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila.
Authors: Cheng, S. / Ashley, J. / Kurleto, J.D. / Lobb-Rabe, M. / Park, Y.J. / Carrillo, R.A. / Ozkan, E.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Structure summary / Category: audit_author
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Defective proboscis extension response 10, isoform A
B: Dpr-interacting protein alpha, isoform A
C: Defective proboscis extension response 10, isoform A
D: Dpr-interacting protein alpha, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60313
Polymers52,3694
Non-polymers4,2349
Water5,332296
1
A: Defective proboscis extension response 10, isoform A
B: Dpr-interacting protein alpha, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1677
Polymers26,1842
Non-polymers2,9835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint45 kcal/mol
Surface area11860 Å2
MethodPISA
2
C: Defective proboscis extension response 10, isoform A
D: Dpr-interacting protein alpha, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4366
Polymers26,1842
Non-polymers1,2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint13 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.011, 53.551, 56.685
Angle α, β, γ (deg.)119.68, 103.77, 92.88
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Defective proboscis extension response 10, isoform A / Defective proboscis extension response 10 / isoform B / isoform C


Mass: 13367.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: dpr10, BcDNA:RE37920, CG14158, CG14159, CT33762, Dmel\CG32057, Dpr-10, Dpr10, CG32057, Dmel_CG32057
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VT83
#2: Protein Dpr-interacting protein alpha, isoform A / Dpr-interacting protein alpha / isoform C / RE16159p


Mass: 12816.413 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: DIP-alpha, 32791, CG13019, CG13020, Dmel\CG32791, CG32791, Dmel_CG32791
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W4R3

-
Sugars , 3 types, 6 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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: isolated from a genetically manipulated source
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

-
Non-polymers , 2 types, 299 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M lithium chloride, 0.1 M HEPES, pH 7.0, 20% (w/v) PEG 6000

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40135 / % possible obs: 86.8 % / Observed criterion σ(I): -3 / Redundancy: 1.82 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.046 / Net I/σ(I): 11.77
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 1.67 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 4014 / CC1/2: 0.67 / Rrim(I) all: 0.721 / % possible all: 53.8

-
Processing

Software
NameVersionClassification
PHENIXdev_3112refinement
XDSNov 11, 2017data reduction
XDSNov 11, 2017data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EO9

5eo9


Resolution: 1.8→48.551 Å / SU ML: 0.23 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / Phase error: 26.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 2002 4.99 %Random
Rwork0.1743 ---
obs0.1759 40105 87.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 282 296 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083811
X-RAY DIFFRACTIONf_angle_d0.9385225
X-RAY DIFFRACTIONf_dihedral_angle_d13.7552231
X-RAY DIFFRACTIONf_chiral_restr0.056642
X-RAY DIFFRACTIONf_plane_restr0.005625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7997-1.84470.5317750.39511416X-RAY DIFFRACTION46
1.8447-1.89460.31671040.31621819X-RAY DIFFRACTION58
1.8946-1.95030.30921090.25962442X-RAY DIFFRACTION78
1.9503-2.01330.30251550.22762782X-RAY DIFFRACTION90
2.0133-2.08520.23261490.20182879X-RAY DIFFRACTION92
2.0852-2.16870.24181550.19032911X-RAY DIFFRACTION93
2.1687-2.26740.2381520.18652946X-RAY DIFFRACTION94
2.2674-2.3870.22671580.18862953X-RAY DIFFRACTION95
2.387-2.53650.21931600.18143010X-RAY DIFFRACTION96
2.5365-2.73230.2531530.18322963X-RAY DIFFRACTION95
2.7323-3.00730.21541590.18113015X-RAY DIFFRACTION96
3.0073-3.44230.17331590.1562984X-RAY DIFFRACTION96
3.4423-4.33650.15471530.14312992X-RAY DIFFRACTION96
4.3365-48.56850.19141610.16472991X-RAY DIFFRACTION96
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)
13.9908-4.16051.94047.2534-2.15474.73880.1257-0.1982-0.58410.1412-0.15720.4159-0.5426-0.06580.09370.3218-0.0786-0.02190.28720.040.245523.2194-24.448331.328
22.721-0.4880.35812.2566-1.49422.87960.0039-0.1563-0.02680.3014-0.0195-0.0775-0.23450.07060.02030.2632-0.00470.00610.30260.03460.212521.9494-33.414438.2399
35.0966-0.3441.26062.4866-1.17154.21030.0215-0.20.06360.2445-0.0685-0.2079-0.24590.2630.0290.2624-0.0259-0.01630.32640.05490.201126.3759-30.784635.234
42.20712.47072.14783.14582.87422.70640.0559-0.1307-1.20370.19140.2553-0.38280.61150.0364-0.5660.40640.0023-0.00270.54210.08970.581217.9433-57.27841.7009
54.0128-3.93655.41285.8551-3.62868.78310.0938-0.5459-0.9899-0.11670.43710.6460.3757-0.863-0.44520.3071-0.0724-0.01050.41560.03510.37181.8122-52.008133.337
64.2072-3.1385.47358.6151-4.48037.37820.09190.1898-0.14070.171-0.4338-0.42780.15120.47440.45590.1909-0.0065-0.00190.40340.09650.288916.2978-48.752244.0069
74.18620.7018-0.72744.477-0.38910.31320.05740.1548-0.01860.1822-0.04720.0958-0.0306-0.01550.02250.19760.00310.0060.33020.05190.15088.0611-43.981940.27
80.96641.49161.24347.6602-3.59347.31591.00972.2962-0.1887-1.3052-0.30810.3441-0.8878-1.727-0.77080.44810.0821-0.05160.75360.05320.34740.831-44.261126.5465
92.8420.76394.98492.85181.21649.0843-0.0494-0.0205-0.21480.0286-0.0512-0.12660.1464-0.27980.07420.23290.01570.01570.31720.02590.225819.4749-47.8438.021
108.64111.89168.75135.23991.82728.8944-0.0902-0.1187-0.62-0.60550.2108-0.1099-0.1204-0.6873-0.00750.3437-0.02190.04990.5375-0.03810.29159.3726-51.84529.0271
119.5294-5.70922.62077.8663-1.20487.9523-0.4556-0.9598-0.21040.78570.409-0.29210.40760.33150.03180.35430.0393-0.02530.39730.05510.255716.2101-25.8120.7571
124.7851.3281-2.09455.8832-0.63836.8463-0.12950.01630.53720.20640.0639-0.0594-0.5952-0.62070.06680.37290.0781-0.0240.35-0.00260.2952-0.9668-11.972111.2376
137.78470.71142.63871.24060.41016.18070.11260.063-0.01660.0412-0.02190.01640.0062-0.0256-0.06650.2278-0.022-0.00520.13060.03580.212410.417-25.17299.5735
147.3398-1.9321-2.78672.79583.18824.06640.37190.85020.2128-0.4274-0.38470.0788-0.272-0.11380.02980.28-0.0029-0.02420.33460.08070.19327.2205-20.7449-1.4758
153.92024.60213.51187.50024.09193.1245-0.32280.89780.92860.2248-0.1291-0.3155-0.80190.64790.47470.3362-0.0372-0.01810.35820.11180.323312.2355-15.61216.0882
163.9841-0.44684.6566.5030.07695.5364-0.79750.49740.34740.27370.3723-0.7894-0.79190.67920.48250.3824-0.0273-0.06280.35570.02680.359513.9865-15.098510.9376
179.07416.8216-5.30236.0679-6.27778.7337-0.0874-0.0145-0.13620.4388-0.1354-0.2107-0.6922-0.11830.08650.27550.0434-0.04170.30860.0430.2515-4.2848-15.2993.9589
185.0209-5.95212.61987.5627-2.26223.0021-0.1567-0.29-0.43980.19520.230.09640.1787-0.0321-0.08260.2951-0.0116-0.01430.26240.04180.23389.5926-29.671912.7227
195.0461-5.88750.02757.3516-1.02547.0076-0.5874-1.1206-0.14070.68360.7630.479-0.2841-0.6952-0.14250.2548-0.058-0.00230.3080.02720.30660.3776-20.418814.9338
205.80992.5648-2.1992.5988-3.10878.1683-0.35021.4995-1.4888-1.59740.13231.05260.0826-1.0743-0.03540.52650.0115-0.16420.9462-0.28310.72940.3648-35.7677-12.5201
214.911.641.45624.2191-1.42226.81690.31691.0146-1.8065-0.68970.25560.77171.06370.6531-0.68220.5035-0.08530.02390.4629-0.25920.67284.4318-50.37190.6269
225.2784-3.94633.83478.7131-5.81394.36570.1890.4432-0.6314-0.9338-0.4894-0.0670.9026-0.18010.26770.44340.0682-0.07120.4418-0.23660.71649.8866-47.2004-2.2556
233.5914-0.77520.1794.28880.20753.60290.26380.7506-0.4793-0.4132-0.1525-0.11930.2431-0.034-0.17580.27090.0138-0.0390.2916-0.0940.27512.2199-37.0721-1.9218
247.5498-4.1277-4.38585.02253.81194.9866-0.7169-1.2944-1.3821.03050.5175-0.08591.59380.46660.34010.57780.0461-0.09490.34750.04580.76711.8869-48.697910.9164
253.919-1.66282.61319.9022-6.33648.48780.03630.4023-0.2991-0.4456-0.2655-0.0470.4426-0.28520.15690.2672-0.0382-0.04870.2879-0.07990.26242.734-33.0669-1.7125
267.4619-5.82734.88719.4109-6.57747.42520.8509-0.3556-1.38-0.52970.37472.07781.0545-0.1255-1.33060.4567-0.095-0.1310.3485-0.0470.64084.5662-48.66865.5603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 156 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 50 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 111 )
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 131 )
10X-RAY DIFFRACTION10chain 'B' and (resid 132 through 142 )
11X-RAY DIFFRACTION11chain 'C' and (resid 48 through 61 )
12X-RAY DIFFRACTION12chain 'C' and (resid 62 through 73 )
13X-RAY DIFFRACTION13chain 'C' and (resid 74 through 98 )
14X-RAY DIFFRACTION14chain 'C' and (resid 99 through 108 )
15X-RAY DIFFRACTION15chain 'C' and (resid 109 through 114 )
16X-RAY DIFFRACTION16chain 'C' and (resid 115 through 124 )
17X-RAY DIFFRACTION17chain 'C' and (resid 125 through 132 )
18X-RAY DIFFRACTION18chain 'C' and (resid 133 through 144 )
19X-RAY DIFFRACTION19chain 'C' and (resid 145 through 155 )
20X-RAY DIFFRACTION20chain 'D' and (resid 40 through 46 )
21X-RAY DIFFRACTION21chain 'D' and (resid 47 through 54 )
22X-RAY DIFFRACTION22chain 'D' and (resid 55 through 66 )
23X-RAY DIFFRACTION23chain 'D' and (resid 67 through 111 )
24X-RAY DIFFRACTION24chain 'D' and (resid 112 through 119 )
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 131 )
26X-RAY DIFFRACTION26chain 'D' and (resid 132 through 144 )

+
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