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- PDB-5ao2: Crystal structure of human SAMHD1 (amino acid residues 115-583) R... -

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Basic information

Entry
Database: PDB / ID: 5ao2
TitleCrystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to dGTP
ComponentsDEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
KeywordsHYDROLASE / DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE / HIV RESTRICTION FACTOR
Function / homology
Function and homology information


Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / dGTP binding / triphosphoric monoester hydrolase activity / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / dGTP catabolic process / DNA strand resection involved in replication fork processing / deoxyribonucleotide catabolic process / regulation of innate immune response / negative regulation of type I interferon-mediated signaling pathway / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / single-stranded DNA binding / site of double-strand break / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2760 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. ...Alpha-Beta Plaits - #2760 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / Sterile alpha motif. / HD/PDEase domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.966 Å
AuthorsSchwefel, D. / Taylor, I.A.
CitationJournal: Plos Pathog. / Year: 2015
Title: Phospho-Dependent Regulation of Samhd1 Oligomerisation Couples Catalysis and Restriction.
Authors: Arnold, L.H. / Groom, H.C.T. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / ...Authors: Arnold, L.H. / Groom, H.C.T. / Kunzelmann, S. / Schwefel, D. / Caswell, S.J. / Ordonez, P. / Mann, M.C. / Rueschenbaum, S. / Goldstone, D.C. / Pennell, S. / Howell, S.A. / Stoye, J.P. / Webb, M. / Taylor, I.A. / Bishop, K.N.
History
DepositionSep 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
B: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
C: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
D: DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,44412
Polymers227,1924
Non-polymers2,2528
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-18.8 kcal/mol
Surface area86280 Å2
MethodPQS PISA
Unit cell
Length a, b, c (Å)69.706, 199.320, 81.804
Angle α, β, γ (deg.)90.00, 100.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 / DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM ...DNTPASE / DENDRITIC CELL-DERIVED IFNG-INDUCED PROTEIN / DCIP / MONOCYTE PROTEIN 5 / MOP-5 / SAM DOMAIN AND HD DOMAIN-CONTAINING PROTEIN 1 / SAMHD1


Mass: 56797.988 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 115-583 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsR164A VARIANT

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM CITRATE, 0.1 M BIS TRIS PROPANE-HCL, 20% PEG 3350, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.97→30 Å / Num. obs: 43467 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / Biso Wilson estimate: 64.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.06
Reflection shellResolution: 2.97→3.14 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.96 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1N
Resolution: 2.966→29.564 Å / SU ML: 0.42 / σ(F): 2 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 2197 5.1 %
Rwork0.1562 --
obs0.1601 43459 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.8 Å2
Refinement stepCycle: LAST / Resolution: 2.966→29.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13474 0 128 4 13606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114451
X-RAY DIFFRACTIONf_angle_d1.50119512
X-RAY DIFFRACTIONf_dihedral_angle_d17.8315467
X-RAY DIFFRACTIONf_chiral_restr0.0682063
X-RAY DIFFRACTIONf_plane_restr0.0082497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9664-3.03090.3643700.25491555X-RAY DIFFRACTION57
3.0309-3.10130.30391280.25062583X-RAY DIFFRACTION98
3.1013-3.17880.35481080.24282586X-RAY DIFFRACTION94
3.1788-3.26460.3341580.2212607X-RAY DIFFRACTION98
3.2646-3.36050.30371450.21522674X-RAY DIFFRACTION100
3.3605-3.46880.28071530.19542649X-RAY DIFFRACTION100
3.4688-3.59260.23511450.17572644X-RAY DIFFRACTION100
3.5926-3.73620.23051410.14982682X-RAY DIFFRACTION99
3.7362-3.90590.20481290.14412713X-RAY DIFFRACTION99
3.9059-4.11130.25121460.13142649X-RAY DIFFRACTION99
4.1113-4.36810.19191360.12512664X-RAY DIFFRACTION99
4.3681-4.70410.19331470.11992551X-RAY DIFFRACTION96
4.7041-5.17530.22061500.12312662X-RAY DIFFRACTION99
5.1753-5.91890.25041590.152678X-RAY DIFFRACTION100
5.9189-7.43750.20771390.16682698X-RAY DIFFRACTION100
7.4375-29.56520.20041430.13932667X-RAY DIFFRACTION98
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)
10.05930.0770.00960.1131-0.00340.086-0.0459-0.09520.05780.01230.11320.10250.0032-0.09780.00030.19950.0119-0.0290.21040.1270.210213.36696.350813.6084
20.2044-0.17590.07290.3605-0.14440.07770.13050.08860.0367-0.2692-0.03690.11840.2468-0.16230.04450.3242-0.0678-0.07920.30570.05550.257114.1596-7.61166.3528
30.1583-0.0254-0.0140.02830.06620.1777-0.0350.1432-0.0115-0.1110.01690.18660.0157-0.1995-0.1240.3578-0.1469-0.19740.42270.15020.34443.07620.683-1.9844
40.00290.00770.0020.13480.1050.09030.02690.09870.0385-0.10780.0592-0.01220.048-0.0490.07650.2481-0.0167-0.01630.32790.09970.199216.832110.00962.5689
50.34960.0716-0.09010.3008-0.17210.1458-0.05880.4787-0.0433-0.48110.159-0.11040.2508-0.07870.05230.3247-0.0337-0.02550.13240.12770.183924.8181-0.14315.9969
60.15550.11920.03210.11120.05870.0592-0.18160.02860.0968-0.28660.23890.0924-0.01650.04850.01780.33120.06160.04660.22090.05930.243341.3258-9.06012.8158
70.08090.16740.03040.37960.13560.11770.0531-0.0042-0.1695-0.05520.0345-0.34320.25480.08860.02410.41920.05320.04350.22250.09840.208843.5313-14.0034-7.7088
80.06610.06830.08510.16320.03780.08450.00460.16860.1167-0.22710.12560.0256-0.1011-0.02020.08390.17260.2710.09060.22960.2270.276426.774110.5859-5.2772
90.04010.00290.04810.0332-0.01860.1746-0.1617-0.0143-0.0539-0.0552-0.10390.0067-0.03250.0283-0.18180.328-0.00620.23570.2116-0.13070.108649.611-7.1386-10.0841
100.2961-0.0681-0.0530.3344-0.08810.21290.1369-0.1539-0.03620.1044-0.1693-0.0882-0.02980.19560.00320.2337-0.0351-0.0540.29910.11160.282544.35172.395432.3122
110.04050.0253-0.05510.2113-0.14840.4480.01-0.07150.08810.12990.02-0.239-0.22810.2739-0.04130.313-0.03840.02770.2702-0.09010.316238.986320.859737.3423
120.9006-0.2004-0.06150.1902-0.12560.0636-0.0464-0.5375-0.02860.10580.09680.0490.1109-0.20270.05310.20170.0071-0.01080.24450.1650.182322.6374-10.419936.6373
130.602-0.61090.16720.7054-0.02550.3880.0929-0.0509-0.32580.09190.12970.28120.0898-0.37470.02430.22890.07830.0090.54260.10720.0819.3738-2.527949.4156
140.0070.00860.00150.1112-0.08950.11590.0420.0587-0.112-0.09510.0997-0.037-0.02580.08710.05010.208-0.00350.02580.267-0.12490.295340.417643.952116.0953
150.04420.0173-0.01150.1241-0.05080.01840.09390.06750.0661-0.05910.02570.1070.0047-0.01640.01620.4198-0.01630.1050.2102-0.00830.312630.245661.6056.8509
160.44810.12080.12140.5223-0.04830.11060.03840.29580.0365-0.37040.0909-0.0649-0.07930.16430.05140.2175-0.05120.10320.209-0.11270.225640.784843.00274.6057
170.00720.0004-0.02020.0287-0.06450.15870.09890.0030.3530.03410.0045-0.1229-0.26870.02960.08970.40130.04880.02950.0798-0.05750.406124.207665.769212.5351
180.0097-0.00370.00950.008-0.00410.0023-0.0349-0.0051-0.02460.02760.052-0.0296-0.1121-0.00080.00010.4702-0.02380.0070.2211-0.06280.431229.374966.41719.379
190.4080.1146-0.21620.1189-0.19710.3040.1053-0.09940.25720.00940.07080.0442-0.3019-0.04920.08860.37740.0941-0.06740.2210.00520.256913.588162.19047.9696
200.42660.18570.14630.53880.16760.078-0.159-0.00060.1565-0.032-0.06420.1003-0.2167-0.0487-0.03490.53120.2031-0.03880.31020.0950.130313.873366.8995-2.1673
210.1424-0.00030.10380.1113-0.05990.12410.00070.08520.0058-0.12890.1139-0.01460.0809-0.0793-0.01260.28330.25990.03140.2063-0.2539-0.11426.927641.7167-3.8411
220.04780.0135-0.01210.0209-0.0040.0062-0.05490.10510.02-0.0901-0.01680.0355-0.01860.0229-0.01080.55120.2827-0.58390.56570.05730.18685.20960.8702-6.7432
230.0799-0.0446-0.09230.02780.03310.19210.1312-0.21120.06220.0467-0.15590.06390.1455-0.23050.00890.1775-0.04730.03310.2703-0.12170.304410.326248.409132.5652
240.0139-0.0073-0.02020.00130.01770.0538-0.042-0.0309-0.02030.0656-0.0387-0.00770.0347-0.0029-0.0688-0.1169-0.40540.26670.4351-0.20390.3001-0.640847.085744.6028
250.0026-0.01140.01140.1124-0.08410.0689-0.0882-0.24260.04670.1338-0.19880.13490.1151-0.2277-0.05630.2841-0.07640.0850.388-0.08760.34811.957837.190338.0666
260.02660.0651-0.03590.1776-0.04550.2031-0.0257-0.0958-0.1560.2731-0.12890.05420.3124-0.1594-0.07010.4792-0.12890.0210.2347-0.01790.258714.2927.362537.791
270.6566-0.0292-0.01240.18960.1960.1756-0.0669-0.7595-0.0570.00670.0705-0.16790.03660.14510.00360.2036-0.0538-0.00620.282-0.16830.20831.236358.270640.6126
280.1405-0.00590.09220.43980.08170.07150.077-0.22390.11370.11350.1372-0.2077-0.11460.33910.13630.0631-0.0143-0.14720.6196-0.18550.063943.106550.923551.0879
290.41650.1041-0.27860.1941-0.17570.2518-0.03450.0183-0.2075-0.0557-0.0447-0.11240.11880.0552-0.01840.13470.1333-0.15680.5924-0.234-0.036445.730845.808254.9216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 115 THROUGH 205 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 206 THROUGH 260 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 261 THROUGH 291 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 292 THROUGH 323 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 324 THROUGH 438 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 439 THROUGH 469 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 470 THROUGH 504 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 505 THROUGH 558 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 559 THROUGH 582 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 115 THROUGH 323 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 324 THROUGH 372 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 373 THROUGH 482 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 483 THROUGH 582 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 115 THROUGH 205 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 206 THROUGH 232 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 233 THROUGH 372 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 373 THROUGH 411 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 412 THROUGH 435 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 436 THROUGH 469 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 470 THROUGH 504 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 505 THROUGH 558 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 559 THROUGH 582 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 115 THROUGH 260 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 261 THROUGH 291 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 292 THROUGH 323 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 324 THROUGH 372 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 373 THROUGH 481 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 482 THROUGH 558 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 559 THROUGH 582 )

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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

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