[English] 日本語
Yorodumi
- PDB-4hg6: Structure of a cellulose synthase - cellulose translocation inter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hg6
TitleStructure of a cellulose synthase - cellulose translocation intermediate
Components
  • Cellulose Synthase Subunit A
  • Cellulose Synthase Subunit B
KeywordsTRANSFERASE / Membrane translocation / cellulose synthesis / UDP-Glc binding / Membrane
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-glucose metabolic process / cyclic-di-GMP binding / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Glycosyltransferase like family 2 / Cellulose synthase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Glycosyltransferase like family 2 / Cellulose synthase / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Glycosyl transferase family 2 / Chitobiase; domain 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Galactose-binding domain-like / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thrombin, subunit H / Jelly Rolls / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Cellulose synthase catalytic subunit [UDP-forming] / Cyclic di-GMP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsZimmer, J.
CitationJournal: Nature / Year: 2012
Title: Crystallographic snapshot of cellulose synthesis and membrane translocation.
Authors: Morgan, J.L. / Strumillo, J. / Zimmer, J.
History
DepositionOct 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_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_unobs_or_zero_occ_atoms.label_asym_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.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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulose Synthase Subunit A
B: Cellulose Synthase Subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,5596
Polymers164,7592
Non-polymers3,8004
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint-5 kcal/mol
Surface area60890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.120, 103.120, 468.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Cellulose Synthase Subunit A /


Mass: 89957.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: RHOS4_19410, RSP_0333 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J125
#2: Protein Cellulose Synthase Subunit B /


Mass: 74801.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: RHOS4_19400, RSP_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2936.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,18,17/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1_l4-m1_m4-n1_n4-o1_o4-p1_p4-q1_q4-r1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}}}}}}}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 30% PEG200, 50mM NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 4, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 47357 / Num. obs: 41133 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.25→3.42 Å / % possible all: 99

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.25→34.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 54.781 / SU ML: 0.419 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28172 2055 5 %RANDOM
Rwork0.21284 ---
all0.2186 41133 --
obs0.21622 39037 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.717 Å2
Baniso -1Baniso -2Baniso -3
1-4.5 Å2-0 Å2-0 Å2
2--4.5 Å20 Å2
3----8.99 Å2
Refinement stepCycle: LAST / Resolution: 3.25→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10780 0 249 0 11029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211325
X-RAY DIFFRACTIONr_angle_refined_deg1.3692.01215489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48351401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31922.352455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.369151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.86315112
X-RAY DIFFRACTIONr_chiral_restr0.090.21814
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0228495
X-RAY DIFFRACTIONr_mcbond_it8.8321.57039
X-RAY DIFFRACTIONr_mcangle_it13.262211361
X-RAY DIFFRACTIONr_scbond_it17.93434286
X-RAY DIFFRACTIONr_scangle_it24.4264.54127
X-RAY DIFFRACTIONr_rigid_bond_restr8.107111325
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 157 -
Rwork0.261 2808 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0496-0.0134-0.0920.04370.05170.2162-0.04070.04370.01370.0286-0.02040.0230.0761-0.08030.06110.2258-0.03610.00820.2541-0.00010.1992-14.336755.565591.201
26.31672.77132.44411.57450.92531.0190.8612-0.5384-0.71340.3299-0.4642-0.21350.4571-0.1625-0.3970.5137-0.0813-0.11350.1850.07510.1594-3.525529.900562.487
30.5025-0.35170.35040.3267-0.47820.92920.00710.2376-0.0972-0.063-0.07660.02520.1257-0.09270.06960.2633-0.01160.00570.3186-0.02630.14771.7845.865746.7918
42.0174-0.9639-0.53520.82460.0180.32510.21690.33510.2572-0.2539-0.1126-0.05860.009-0.0368-0.10430.2848-0.02770.01410.31660.0670.13161.759560.807137.0325
50.09430.7991-0.43186.8644-3.70942.0064-0.03770.01050.0214-0.14920.09480.08010.0796-0.0835-0.05710.14770.0104-0.03190.3497-0.00140.1422-9.96752.775744.0763
60.0064-0.00140.00970.002-0.00770.4193-0.0150.0140.0274-0.00580.0128-0.01390.0809-0.00830.00210.2435-0.02240.00580.25290.00340.1758-0.763446.886463.4763
70.63771.1991.93022.36593.73645.9619-0.1393-0.065-0.0289-0.67760.2267-0.0819-0.98150.0169-0.08730.5594-0.30480.11640.6028-0.05830.5222-18.575149.285951.0612
80.021-0.0276-0.05910.04310.09260.27390.04110.05-0.0054-0.03-0.0554-0.02490.008-0.10410.01430.2527-0.0154-0.01080.289-0.00380.2051-8.665348.462160.44
93.54720.3380.24170.33880.29280.3250.2083-0.0579-0.2186-0.0903-0.19-0.0286-0.004-0.1145-0.01830.22140.0151-0.02360.28190.0130.1778-9.00562.476764.0166
100.17850.0118-0.13410.0026-0.00530.1126-0.01340.04280.03590.0164-0.0040.01040.0301-0.04550.01740.2392-0.0124-0.00210.24520.01790.211-9.230164.229984.4178
110.5286-0.30680.09320.5416-0.04360.05170.00350.1056-0.0677-0.0509-0.03480.0280.03780.05480.03130.2194-0.012-0.01750.24340.02130.1796-4.027265.835772.2407
122.51892.9561-2.46193.4709-2.88962.4095-0.16380.22150.3121-0.30570.36910.34870.2409-0.185-0.20530.2752-0.1301-0.07760.8162-0.20860.38352.058971.114455.9841
130.1231-0.0345-0.37510.16590.20421.2644-0.0196-0.01280.0342-0.0160.061-0.0496-0.00580.0624-0.04140.2075-0.02570.00760.24940.02140.22486.2176.476881.9554
140.39180.08770.5321.2848-0.45120.98140.010.0997-0.013-0.1267-0.0338-0.13030.07430.15340.02380.23490.02390.05240.280.03120.154330.636342.990952.9611
150.2531-0.06620.01720.0472-0.02320.0444-0.06140.06630.00160.0339-0.0039-0.06540.0706-0.03040.06530.283-0.01870.03530.25540.00790.165613.473244.59661.5416
160.2721-0.0528-0.08970.08780.18070.38940.0275-0.02210.0243-0.0110.029-0.0322-0.06130.1089-0.05640.2051-0.02440.01350.24470.01740.216917.097172.871173.6017
171.83721.46140.26891.1690.20830.0548-0.09440.18970.0984-0.06150.08470.03440.03110.11280.00980.41160.16650.03010.50930.19780.330321.116961.181649.618
182.8727-0.1454-1.57980.0214-0.11785.15260.13150.24940.08030.0004-0.01140.01090.4921-0.2656-0.12010.3266-0.00990.01260.1493-0.01860.1849-20.193983.441148.132
190.88380.8402-0.73441.0504-0.85530.7440.3093-0.00460.51590.2840.01530.3555-0.22370.1065-0.32450.2797-0.00980.14550.35560.02650.3798-17.119795.3627143.5911
201.41541.1908-1.34191.0034-1.12211.67050.2277-0.04740.07850.1828-0.0490.0649-0.21550.1958-0.17870.2101-0.00430.05450.24940.00050.1458-10.809192.3777141.0855
210.01590.0226-0.01020.0331-0.01210.01130.03150.00920.06060.05420.01260.0810.0103-0.019-0.0440.23970.01130.03640.2644-0.00250.2623-30.56182.7773156.2263
220.45280.0279-0.40950.3687-0.09160.391-0.05070.0075-0.02370.01750.0498-0.00760.05110.01870.00080.24050.00230.03470.26080.01720.176-31.586270.1956156.905
234.27331.8369-0.53350.87270.23022.61210.05460.23940.01510.01710.0754-0.0145-0.0334-0.223-0.130.22590.00560.05840.21230.02290.1336-41.717171.9783162.9991
240.19110.21740.21630.25540.25520.2892-0.02850.00470.0356-0.0112-0.01230.0638-0.0589-0.11160.04080.15910.07040.07170.3360.06090.1584-37.284878.7993138.245
250.28240.21220.05680.28370.19540.2269-0.00750.0068-0.0254-0.00070.0108-0.0127-0.0576-0.0426-0.00340.23070.0016-0.00540.2320.02240.205-15.613486.2068117.036
260.28670.1209-0.18750.07010.06011.1478-0.00070.02630.00860.03270.01020.0080.1989-0.0331-0.00940.2501-0.00970.01890.25350.010.171-29.263861.4014138.1026
270.02-0.5712-0.279417.97458.68054.20390.0630.0501-0.02460.1897-0.50320.83760.097-0.35980.44020.83540.0741-0.02110.80430.0460.0472-16.704446.6443133.6319
2822.2408-10.51043.57396.437-6.074613.6583-0.07120.0150.8539-0.3675-0.3115-0.4751.23021.00750.38270.4350.07450.0790.2905-0.05560.0707-7.920655.8576142.7786
291.7960.5452-1.49520.2162-0.72042.8577-0.2605-0.0696-0.0035-0.1169-0.0087-0.06670.36410.17560.26920.25730.04080.03330.22630.0030.1922-7.184367.7545117.2285
300.48670.6992-0.41722.32940.28460.95870.1055-0.0996-0.02990.4182-0.1303-0.11880.09220.09060.02470.27610.0027-0.02620.23940.03850.1973-2.065557.8548114.3845
314.6285-2.0081-1.47731.7123-1.45475.77670.43230.30550.2152-0.279-0.2681-0.0939-0.03690.1094-0.16420.23690.10.07560.30230.05520.127-7.734356.81132.4613
321.0622-0.70360.41820.69540.24091.5713-0.01450.05240.05420.0014-0.047-0.07540.1658-0.020.06150.22760.00060.02880.2409-0.00080.1565-19.9964.0514136.5169
331.38960.939-0.31222.21230.86290.8021-0.10040.00260.02430.2139-0.10960.32430.2321-0.08740.210.2431-0.0770.0840.29020.0270.136-29.407156.8181112.9216
341.2661-1.5251.8862.7002-0.94644.8551-0.0548-0.06720.01530.1005-0.0351-0.0063-0.0133-0.27940.08990.2032-0.05490.03830.27070.02530.1936-24.410458.7553107.4341
350.11130.1395-0.30730.2528-0.55051.2149-0.0897-0.0439-0.0483-0.05960.0245-0.02310.1866-0.10660.06520.2916-0.05480.05060.2376-0.00590.1843-16.019242.350693.4981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 125
2X-RAY DIFFRACTION2A126 - 136
3X-RAY DIFFRACTION3A137 - 181
4X-RAY DIFFRACTION4A182 - 221
5X-RAY DIFFRACTION5A222 - 239
6X-RAY DIFFRACTION6A240 - 325
7X-RAY DIFFRACTION7A326 - 339
8X-RAY DIFFRACTION8A340 - 370
9X-RAY DIFFRACTION9A371 - 399
10X-RAY DIFFRACTION10A400 - 468
11X-RAY DIFFRACTION11A469 - 499
12X-RAY DIFFRACTION12A500 - 513
13X-RAY DIFFRACTION13A514 - 579
14X-RAY DIFFRACTION14A580 - 678
15X-RAY DIFFRACTION15A679 - 707
16X-RAY DIFFRACTION16A708 - 746
17X-RAY DIFFRACTION17A747 - 759
18X-RAY DIFFRACTION18B54 - 70
19X-RAY DIFFRACTION19B71 - 148
20X-RAY DIFFRACTION20B149 - 187
21X-RAY DIFFRACTION21B188 - 208
22X-RAY DIFFRACTION22B209 - 255
23X-RAY DIFFRACTION23B256 - 292
24X-RAY DIFFRACTION24B293 - 315
25X-RAY DIFFRACTION25B316 - 449
26X-RAY DIFFRACTION26B450 - 511
27X-RAY DIFFRACTION27B512 - 520
28X-RAY DIFFRACTION28B521 - 531
29X-RAY DIFFRACTION29B544 - 569
30X-RAY DIFFRACTION30B570 - 595
31X-RAY DIFFRACTION31B596 - 610
32X-RAY DIFFRACTION32B611 - 666
33X-RAY DIFFRACTION33B667 - 679
34X-RAY DIFFRACTION34B680 - 693
35X-RAY DIFFRACTION35B694 - 720

+
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