[English] 日本語
Yorodumi
- PDB-4ymd: CL-K1 trimer bound to man(alpha1-2)man -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ymd
TitleCL-K1 trimer bound to man(alpha1-2)man
ComponentsCollectin-11
KeywordsSUGAR BINDING PROTEIN / C-type carbohydrate-recognition domain / collectin / C-type lectin
Function / homology
Function and homology information


calcium-dependent carbohydrate binding / Lectin pathway of complement activation / positive regulation of opsonization / fucose binding / complement activation, lectin pathway / oligosaccharide binding / developmental process / cell surface pattern recognition receptor signaling pathway / collagen trimer / antimicrobial humoral response ...calcium-dependent carbohydrate binding / Lectin pathway of complement activation / positive regulation of opsonization / fucose binding / complement activation, lectin pathway / oligosaccharide binding / developmental process / cell surface pattern recognition receptor signaling pathway / collagen trimer / antimicrobial humoral response / serine-type endopeptidase complex / complement activation / Scavenging by Class A Receptors / execution phase of apoptosis / Initial triggering of complement / D-mannose binding / external side of plasma membrane / calcium ion binding / proteolysis / DNA binding / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Collectin, C-type lectin-like domain / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
2alpha-alpha-mannobiose / Collectin-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsWallis, R. / Venkatraman Girija, U. / Gingras, A.R. / Moody, P.C.E. / Marshall, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000191/1 United Kingdom
CitationJournal: Bmc Biol. / Year: 2015
Title: Molecular basis of sugar recognition by collectin-K1 and the effects of mutations associated with 3MC syndrome.
Authors: Girija, U.V. / Furze, C.M. / Gingras, A.R. / Yoshizaki, T. / Ohtani, K. / Marshall, J.E. / Wallis, A.K. / Schwaeble, W.J. / El-Mezgueldi, M. / Mitchell, D.A. / Moody, P.C. / Wakamiya, N. / Wallis, R.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: 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 3.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collectin-11
B: Collectin-11
D: Collectin-11
F: Collectin-11
C: Collectin-11
E: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,61635
Polymers103,8816
Non-polymers2,73529
Water27015
1
A: Collectin-11
B: Collectin-11
C: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35418
Polymers51,9403
Non-polymers1,41415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-131 kcal/mol
Surface area23420 Å2
MethodPISA
2
D: Collectin-11
F: Collectin-11
E: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,26217
Polymers51,9403
Non-polymers1,32214
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-126 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.850, 106.650, 78.390
Angle α, β, γ (deg.)90.000, 92.170, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA116 - 306
211chain BB116 - 306
311chain CC117 - 306
411chain DD116 - 306
511chain EE122 - 306
611chain FF116 - 306

-
Components

#1: Protein
Collectin-11 / Collectin kidney protein 1 / CL-K1


Mass: 17313.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COLEC11, UNQ596/PRO1182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BWP8
#2: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES, 10% v/v ethanol and 4 mM calcium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.87→44.08 Å / Num. obs: 24670 / % possible obs: 91 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.2
Reflection shellResolution: 2.87→2.973 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2518 / % possible all: 93.57

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLI

4yli


Resolution: 2.87→44.08 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1232 4.99 %
Rwork0.213 23435 -
obs0.2157 24667 91.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.66 Å2 / Biso mean: 95.4811 Å2 / Biso min: 37.16 Å2
Refinement stepCycle: final / Resolution: 2.87→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 152 15 7329
Biso mean--106.8 65.67 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047425
X-RAY DIFFRACTIONf_angle_d0.8539966
X-RAY DIFFRACTIONf_chiral_restr0.0361072
X-RAY DIFFRACTIONf_plane_restr0.0031297
X-RAY DIFFRACTIONf_dihedral_angle_d13.6922805
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4426X-RAY DIFFRACTION8.983TORSIONAL
12B4426X-RAY DIFFRACTION8.983TORSIONAL
13C4426X-RAY DIFFRACTION8.983TORSIONAL
14D4426X-RAY DIFFRACTION8.983TORSIONAL
15E4426X-RAY DIFFRACTION8.983TORSIONAL
16F4426X-RAY DIFFRACTION8.983TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8701-2.9850.38261360.33932656279293
2.985-3.12080.37291300.31172408253885
3.1208-3.28530.34131160.29062524264088
3.2853-3.4910.32681590.26262736289597
3.491-3.76040.34171380.22882751288996
3.7604-4.13860.24951360.20382681281793
4.1386-4.73690.28611300.17852371250183
4.7369-5.96560.20831500.18532727287795
5.9656-44.08580.211370.18792581271889
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)
10.05130.1180.08690.19960.17930.1337-0.01510.83290.0002-0.22950.30440.31790.06110.06750.00470.8095-0.1555-0.05690.6393-0.16111.03341.4692-8.604811.4669
20.3312-0.1823-0.13620.14780.04140.07360.5946-0.0126-0.46730.40150.50560.9832-0.2540.33-0.0351.0748-0.01850.06840.8712-0.18030.893534.2003-27.546918.8207
31.08461.208-0.51822.0207-0.74750.2772-0.1976-0.09140.1973-0.36390.33070.1797-0.1190.5008-0.00020.638-0.12380.09410.5024-0.24460.616334.0694-39.467917.6245
40.47680.1553-0.59063.0633-0.57051.9121-0.2973-0.2962-0.39910.17150.08310.53-0.14420.20030.01110.494-0.20780.09070.6259-0.15760.617131.004-48.491222.3486
50.12510.174-0.07630.2247-0.10680.0367-0.26160.04460.02990.44490.232-0.04030.39610.09360.00010.8401-0.2098-0.02020.5567-0.16670.693746.3905-15.43218.8392
60.9412-0.2637-1.04210.22160.30121.11280.0363-0.08340.07450.6984-0.64280.1519-0.4332-0.431-0.58830.7447-0.7414-0.2282-0.0226-0.76210.372545.0251-33.6179-0.9495
70.08810.1823-0.12850.9141-0.50920.27550.38641.07820.1338-0.0503-0.85190.1943-0.3972-0.1010.00010.781-0.0731-0.02450.7822-0.1640.698445.4586-31.8225-10.8656
80.0670.0363-0.06960.2803-0.18760.1580.0649-0.8790.02531.73820.2462-0.4855-0.06080.9350.00070.8596-0.27240.00080.8154-0.05980.66251.8382-41.00690.0482
91.8096-0.37930.73961.52290.70982.08480.4730.35970.0966-0.0852-0.5036-0.1032-0.01520.0725-0.00660.4927-0.16690.09540.5858-0.11760.456449.4815-41.3061-14.3804
100.2423-0.3558-0.34540.51720.2610.45510.4860.2469-0.44580.04390.0053-0.42780.1378-0.93970.01080.61450.0601-0.23140.60910.19950.732110.5325-49.696448.2444
111.98332.21770.05812.8713-1.15541.8186-0.0618-0.10690.04950.1662-0.02960.0930.12940.4912-0.00030.64790.10480.11590.59080.07980.450418.1672-19.518332.9003
120.76710.99920.04441.89620.76180.8654-0.00650.01420.1538-0.43470.08960.47420.09270.54230.00120.5850.11030.12030.84020.13810.617117.2978-13.643227.8434
130.59490.43120.08450.3015-0.01050.33250.10790.22830.5988-0.2029-0.0926-1.16910.3437-0.1251-0.00070.79910.1054-0.01170.46050.06810.865118.8222-41.79751.7883
140.6458-0.1505-0.31871.13240.3670.23330.55130.28310.2048-0.4666-0.5044-0.78590.98460.1792-0.0010.62830.10560.02890.68580.05040.4959-1.0708-24.402348.577
152.0351-1.0837-0.85221.6304-0.19580.83880.80390.32530.2824-0.2407-0.616-0.2497-0.11040.01670.00020.51550.02560.01610.50980.07440.5447-6.7997-20.208551.3633
160.7148-0.537-0.27940.3820.28450.9370.5332-0.58450.15710.6652-0.02610.1924-0.0656-0.24650.00050.5668-0.06760.13560.51640.07350.8349-16.4975-14.463459.3668
170.2008-0.15140.06820.1238-0.09220.1033-0.1915-0.0030.3569-1.00510.5053-0.40050.3971-0.27280.00010.57620.09370.09390.62010.13220.6379-18.0122-10.447149.8559
180.84530.2574-0.22260.37890.42440.83840.5995-0.0720.333-0.1673-0.28380.0126-0.0817-0.1613-0.00010.56330.06450.01020.58270.04510.5471-9.1224-18.779450.0748
190.07060.1702-0.00870.2488-0.0026-0.016-0.3440.44380.47060.1342-0.25050.80790.30710.4597-0.0010.8981-0.1982-0.14820.769-0.16620.890350.3605-12.6577.8121
200.5212-0.26650.23680.1207-0.1340.90450.15280.39090.24590.67650.6079-0.0979-0.0305-0.32920.06270.6645-0.1498-0.16590.66350.03870.879627.6277-22.72230.9191
211.64250.25161.41550.192-0.02511.54380.3066-0.98750.5145-0.1325-0.33150.1407-0.4701-0.43540.00040.7918-0.0347-0.15490.9518-0.19870.781717.3724-20.11-1.1926
220.21250.0583-0.00830.01260.0043-0.0012-0.7855-0.66460.81440.8180.98530.71380.2127-0.96210.01191.02150.127-0.04741.1478-0.27521.528712.828-10.0357-3.3444
230.32460.06380.22310.22210.09670.16330.4031-0.04080.47240.62290.15380.0690.3682-1.0914-0.01670.7401-0.1043-0.10440.6834-0.12030.8048.3527-20.597-12.3968
240.7256-0.8980.38531.1571-0.10440.91370.0295-0.4670.3670.18410.21530.05430.2309-0.6150.00160.6768-0.1689-0.15330.7355-0.05610.722914.2702-23.7616-2.7626
252.60510.1481-1.32990.1406-0.02970.7834-0.23340.2613-0.35050.15590.21250.4827-0.1564-0.24330.00060.7650.1616-0.05760.69130.01140.75652.021-39.402643.6509
260.2162-0.01440.17160.77060.43192.0467-0.26140.1017-0.0905-0.9416-0.09270.63451.07980.7619-0.05460.90090.0953-0.14661.6396-0.21280.9016-6.5484-41.996323.1514
270.2062-0.2464-0.23920.75490.10090.4269-0.82261.09620.2474-0.35640.21120.4913-0.40610.2345-0.18311.2553-0.2782-0.64310.98890.04121.0715-10.0818-37.634920.703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 116 through 141 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 151 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 196 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 269 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 141 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 162 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 163 through 182 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 196 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 197 through 269 )B0
10X-RAY DIFFRACTION10chain 'D' and (resid 116 through 141 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 142 through 226 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 227 through 270 )D0
13X-RAY DIFFRACTION13chain 'F' and (resid 116 through 141 )F0
14X-RAY DIFFRACTION14chain 'F' and (resid 142 through 162 )F0
15X-RAY DIFFRACTION15chain 'F' and (resid 163 through 206 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 207 through 235 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 236 through 246 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 247 through 269 )F0
19X-RAY DIFFRACTION19chain 'C' and (resid 117 through 141 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 142 through 162 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 163 through 216 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 217 through 226 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 227 through 235 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 236 through 269 )C0
25X-RAY DIFFRACTION25chain 'E' and (resid 122 through 162 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 163 through 226 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 227 through 270 )E0

+
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