[English] 日本語
Yorodumi
- PDB-5m73: Structure of the human SRP S domain with SRP72 RNA-binding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m73
TitleStructure of the human SRP S domain with SRP72 RNA-binding domain
Components
  • (Signal recognition particle subunit ...) x 2
  • Human gene for small cytoplasmic 7SL RNA (7L30.1)
  • Signal recognition particle 19 kDa protein
KeywordsRNA BINDING PROTEIN / protein targeting / signal recognition particle / protein-RNA complex / RNA kink-turn
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane ...SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / nuclear body / ribosome / response to xenobiotic stimulus / protein domain specific binding / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
Signal recognition particle, SRP68 subunit, RNA-binding domain / Hyaluronidase domain-like / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain ...Signal recognition particle, SRP68 subunit, RNA-binding domain / Hyaluronidase domain-like / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle subunit SRP72 / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBecker, M.M.M. / Wild, K. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 638 Germany
German Research FoundationGRK1188 Germany
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction.
Authors: Becker, M.M. / Lapouge, K. / Segnitz, B. / Wild, K. / Sinning, I.
History
DepositionOct 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Derived calculations
Revision 1.3Jan 18, 2017Group: Database references
Revision 1.4Oct 16, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / reflns_shell / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2019Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Human gene for small cytoplasmic 7SL RNA (7L30.1)
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle subunit SRP68
D: Signal recognition particle subunit SRP72
E: Human gene for small cytoplasmic 7SL RNA (7L30.1)
F: Signal recognition particle 19 kDa protein
G: Signal recognition particle subunit SRP68
H: Signal recognition particle subunit SRP72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,23772
Polymers206,9238
Non-polymers2,31464
Water0
1
A: Human gene for small cytoplasmic 7SL RNA (7L30.1)
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle subunit SRP68
D: Signal recognition particle subunit SRP72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,93945
Polymers103,4614
Non-polymers1,47741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Human gene for small cytoplasmic 7SL RNA (7L30.1)
F: Signal recognition particle 19 kDa protein
G: Signal recognition particle subunit SRP68
H: Signal recognition particle subunit SRP72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,29827
Polymers103,4614
Non-polymers83623
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.567, 139.306, 152.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN G AND (RESSEQ 51:68 OR RESSEQ 70:92 OR RESSEQ...
211(CHAIN C AND (RESSEQ 51:68 OR RESSEQ 70:92 OR RESSEQ...
112(CHAIN B AND (RESSEQ 14:57 OR RESSEQ 59:73 OR RESSEQ 75:78 OR RESSEQ 80:88 OR RESSEQ 90:115))
212(CHAIN F AND (RESSEQ 14:57 OR RESSEQ 59:73 OR RESSEQ 75:78 OR RESSEQ 80:88 OR RESSEQ 90:115))
113(CHAIN A AND ((RESID 106 AND (NAME P OR NAME...
213(CHAIN E AND ((RESID 106 AND (NAME P OR NAME...

NCS ensembles :
ID
1
2
3

-
Components

-
Signal recognition particle subunit ... , 2 types, 4 molecules CGDH

#3: Protein Signal recognition particle subunit SRP68 / / SRP68 / Signal recognition particle 68 kDa protein


Mass: 24280.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB9
#4: Protein Signal recognition particle subunit SRP72 / / SRP72 / Signal recognition particle 72 kDa protein


Mass: 17189.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP72 / Production host: Escherichia coli (E. coli) / References: UniProt: O76094

-
RNA chain / Protein , 2 types, 4 molecules AEBF

#1: RNA chain Human gene for small cytoplasmic 7SL RNA (7L30.1)


Mass: 47199.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 23924
#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 14791.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P09132

-
Non-polymers , 3 types, 64 molecules

#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 17 % (w/v) PEG3350 0.1 M KF 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 3.4→48.4 Å / Num. obs: 39893 / % possible obs: 99.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.253 / Net I/σ(I): 8.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p3e

4p3e


Resolution: 3.4→48.39 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.15
RfactorNum. reflection% reflection
Rfree0.28 3638 4.84 %
Rwork0.237 --
obs0.239 39533 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 137.4 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 6243 109 0 12128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112913
X-RAY DIFFRACTIONf_angle_d1.56718812
X-RAY DIFFRACTIONf_dihedral_angle_d17.9717155
X-RAY DIFFRACTIONf_chiral_restr0.0942268
X-RAY DIFFRACTIONf_plane_restr0.0111300
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11G1754X-RAY DIFFRACTIONPOSITIONAL
12C1754X-RAY DIFFRACTIONPOSITIONAL
21B923X-RAY DIFFRACTIONPOSITIONAL
22F923X-RAY DIFFRACTIONPOSITIONAL
31A3324X-RAY DIFFRACTIONPOSITIONAL
32E3324X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.44470.40191090.37322775X-RAY DIFFRACTION98
3.4447-3.49190.45761110.36622737X-RAY DIFFRACTION99
3.4919-3.54180.40721670.3612718X-RAY DIFFRACTION98
3.5418-3.59460.37031470.35182673X-RAY DIFFRACTION98
3.5946-3.65080.39811400.35662756X-RAY DIFFRACTION98
3.6508-3.71060.38751220.35752735X-RAY DIFFRACTION99
3.7106-3.77460.40991500.33772771X-RAY DIFFRACTION99
3.7746-3.84320.38211210.33752741X-RAY DIFFRACTION98
3.8432-3.91710.36031220.31772754X-RAY DIFFRACTION99
3.9171-3.9970.3421420.29852704X-RAY DIFFRACTION98
3.997-4.08390.37321430.29612758X-RAY DIFFRACTION98
4.0839-4.17880.39011370.28592737X-RAY DIFFRACTION99
4.1788-4.28320.31561270.2892755X-RAY DIFFRACTION99
4.2832-4.3990.34781560.27152769X-RAY DIFFRACTION99
4.399-4.52830.31771660.26822734X-RAY DIFFRACTION99
4.5283-4.67440.28491780.2482712X-RAY DIFFRACTION99
4.6744-4.84130.28361720.24552749X-RAY DIFFRACTION99
4.8413-5.03490.30851380.22632750X-RAY DIFFRACTION99
5.0349-5.26380.29331130.21562800X-RAY DIFFRACTION100
5.2638-5.5410.27521260.23212820X-RAY DIFFRACTION100
5.541-5.88760.28041580.21672759X-RAY DIFFRACTION100
5.8876-6.34130.26281780.21332755X-RAY DIFFRACTION100
6.3413-6.97770.241340.212774X-RAY DIFFRACTION100
6.9777-7.98350.21961030.17442828X-RAY DIFFRACTION100
7.9835-10.04360.19371200.16572786X-RAY DIFFRACTION100
10.0436-48.39750.17241580.14422748X-RAY DIFFRACTION99
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)
10.05110.8807-0.23961.0271-0.78972.34340.127-0.08230.3194-0.3925-0.626-0.3997-0.10850.11840.34621.74560.09110.16050.65720.24951.9956-15.499237.0856-20.3686
2-0.4355-0.1209-0.10841.27780.1741-0.47730.3145-0.22920.09440.8924-0.7108-0.0186-0.1645-0.34440.2581.99380.05780.18390.60320.01452.0592-7.9926-21.4144-17.5611
30.4225-1.0832-0.00821.83431.00670.03770.34940.1010.0421-0.7902-0.51160.0148-0.1885-0.26170.10082.07520.06670.20860.60310.11541.9305-11.71631.3088-30.421
41.33360.11860.63112.7222-0.75610.64950.3548-0.1801-0.06470.00680.01480.8047-0.7136-0.8158-0.41692.47220.18840.37440.71530.27692.7605-24.749571.2901-22.2497
56.6079-2.25541.02822.81891.33632.2428-0.2135-0.6166-0.7897-0.4938-0.46150.43010.5637-0.04870.281.8483-0.0040.110.2691-0.02060.95924.3949-37.9954-25.8452
62.8873-2.80590.49843.6872-1.68971.62990.20590.4219-0.4047-0.2703-0.2009-1.25270.7470.3963-0.00591.70210.01991.15380.2895-0.63890.07572.1449-25.7099-24.5126
75.8085-3.7777-0.61297.99524.08096.8402-0.63710.33380.21381.0573-0.1540.5035-1.36420.84660.37471.215-0.02380.08650.43950.12561.210812.9889-35.3998-22.5112
81.7283-0.31850.06013.63982.41751.8487-0.02680.4869-0.7161-1.21080.0598-0.22240.31740.7245-0.2062.32030.24170.2064-0.0858-0.13871.46426.1307-41.4768-28.5719
92.8105-0.3357-1.00340.1792-0.47423.0426-0.0646-0.4832-0.11641.736-0.3743-0.8134-1.08682.0450.22022.18360.24550.03-0.1329-0.17951.590613.3205-38.9744-17.0267
103.50261.8365-0.46113.7266-0.39422.16760.13810.50990.3532-0.6012-0.1593-0.794-0.4731-0.09510.13481.62970.04610.33820.51840.0681.5452-18.906535.2166-10.8968
119.2685-2.0185-5.87476.34646.07949.55450.3283-1.27691.0038-0.7735-0.0108-0.9579-1.65442.1759-0.51951.2043-0.10320.09631.04820.21652.2348-4.380237.76-4.9735
124.54340.9979-0.46443.6262-0.64324.87040.2253-0.46960.0108-0.1248-0.2473-0.2958-0.0650.23970.04271.391-0.06620.05630.45970.11771.2833-19.327926.27912.0626
138.7754-2.25831.29142.4223-1.47924.9522-0.3971-0.3687-0.22840.58260.97481.5888-0.0341-0.3812-0.59451.20970.11060.4620.77410.05331.7765-31.624126.511210.5104
144.48575.09363.37186.03744.3443.5687-0.47621.34710.1808-0.98340.3528-1.5466-0.34960.96230.15611.1875-0.13160.17071.40170.1031.9092-12.498979.7417-25.1403
157.6039-3.4137-1.92521.60680.94880.55820.1538-0.46520.1649-0.95890.1821-1.8268-0.27360.4138-0.14093.0136-0.19140.16060.2105-0.37974.0574-10.555785.2388-32.1314
163.5062-3.4704-1.36444.5885-1.06915.5241-0.11790.58650.86130.0406-0.43781.3004-1.9311-0.50620.16762.03070.046-0.63971.16430.01273.0692-14.93677.3125-38.6147
173.546-4.26970.36666.4495-0.1530.154-0.11340.99770.1517-0.7884-0.33830.73811.2175-0.6280.01512.4993-0.050.28850.47170.1021.8347-9.703156.4001-37.2266
181.71362.1133-1.41882.5202-1.55680.84360.33960.121-0.99430.063-0.86040.65790.64710.34640.54822.64520.12990.04790.8665-0.17352.089-50.4986-28.2223-21.5459
190.81990.003-0.0250.8286-1.37321.26040.67380.08970.51530.7126-0.8529-0.0862-0.5467-0.02880.17652.7815-0.03810.10430.79540.01771.8319-60.984342.83-17.4397
200.8179-2.55070.11337.3055-0.58970.18020.5780.24570.34360.2929-0.35610.7395-0.9398-0.1369-0.18152.208-0.10020.06520.77260.12131.5153-59.302326.234-10.3496
210.7112-2.80020.568.2801-1.19152.10320.1910.16430.2266-0.491-0.5321-0.1811-0.08980.01370.35392.1963-0.05120.33980.84620.21232.0695-55.800544.3726-35.3443
226.3699-4.312-1.52352.93150.09485.19762.0388-0.05380.0858-1.063-2.3727-0.6008-0.20990.16580.31232.9565-0.04180.38071.00920.19511.8705-55.725442.2357-40.0941
234.69961.2432-1.6320.3907-0.89652.65670.45170.4126-0.2637-0.7477-0.6363-0.04620.93030.10620.19122.06310.0373-0.19760.8217-0.0691.5386-54.7518-1.172-26.0246
244.1001-3.3128-0.44143.93751.36141.67290.43770.2082-0.44260.5351-0.75740.11630.1190.38750.23972.7242-0.01730.20620.9687-0.15262.9369-45.4953-42.7042-20.3881
255.0956-1.3823-1.29090.5846-0.45293.5138-0.2079-0.32242.9843-0.61431.18432.4452-1.6211-0.2017-0.78822.61340.41570.48481.02230.10941.9577-70.803967.4923-25.8057
262.3444-1.15070.74273.1281-1.99671.43980.03890.42591.06480.22250.41441.0441-2.1938-1.6391-0.53952.8980.59520.37171.35070.4451.5741-78.249862.2623-25.4335
274.9695-1.2544-0.40080.98681.57445.17820.38920.41920.61881.83810.2659-0.3023-0.151-1.2443-0.6682.18550.21970.20591.0490.27621.727-73.495260.2751-36.707
283.6489-0.8261-2.12460.87740.73761.3761.1308-0.02632.41850.84890.2894-0.8439-1.41190.3681-1.18413.7090.09620.40111.20160.77252.8747-70.587776.5484-22.9543
295.14667.04975.77039.73727.91036.49771.0539-0.80553.44030.2212-0.86960.2458-0.7161-0.0259-0.38072.62160.57590.59561.501-0.0631.886-72.973476.9363-13.0269
300.1958-0.6755-0.31172.79631.85735.8173-0.9721-0.15150.33920.5102-0.70771.3376-0.3924-2.520.31943.25341.12681.07391.28660.9291.5935-82.884263.8121-20.3989
311.4851.61390.76434.21881.52651.69561.23770.6938-1.0173-0.3116-0.10170.1130.22570.3959-0.53451.94690.02840.06220.43080.20041.697-49.7121-8.9369-6.063
325.7713-1.59041.98053.3173-0.42887.85020.23190.79460.1081-1.29080.23520.76430.6962-1.4974-0.57251.44040.0457-0.20120.907-0.0051.8221-68.8358-4.8908-13.4258
336.053-5.72432.49985.8304-1.88241.69410.19250.0286-0.0182-1.17281.19313.18771.8245-1.8116-1.42811.6228-0.146-0.59431.1030.68672.4157-66.338-15.0358-3.1699
343.05463.1975-0.43047.6171-0.72491.99910.31810.3072-0.1264-0.7419-0.0021-0.01430.11340.274-0.01172.0372-0.05540.13980.168-0.03221.3326-53.04944.2929-3.2529
355.05992.0613-0.06884.8876-0.57873.50.0041-0.5769-0.53720.27450.0415-0.92220.0431-0.1365-0.03351.4837-0.3021-0.19020.5580.03441.1529-48.9717-0.84611.8098
360.55090.62-1.73291.1099-2.60746.4942-0.0983-0.1665-0.29770.1094-0.1363-0.13620.19570.11980.13672.28410.06110.07551.8073-0.04511.146-57.3738-51.412-24.4262
376.1703-2.11041.66444.8332-2.48993.30861.1590.562-2.02290.40450.5281.432.60680.873-1.22351.7387-0.162-0.39841.3090.18932.6222-54.2976-50.377-35.096
382.82710.3301-0.20832.5673-2.09631.5391-1.15031.6990.0973-0.1312-0.2538-0.8028-2.6572-0.37331.02771.93370.1295-0.28991.2506-0.26721.1876-60.5115-26.8896-36.4394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 106 THROUGH 135 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 136 THROUGH 165 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 166 THROUGH 235 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 236 THROUGH 249 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 11 THROUGH 28 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 29 THROUGH 33 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 34 THROUGH 56 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 57 THROUGH 94 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 95 THROUGH 118 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 50 THROUGH 99 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 100 THROUGH 114 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 115 THROUGH 218 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 219 THROUGH 246 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 557 THROUGH 561 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 562 THROUGH 567 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 568 THROUGH 576 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 577 THROUGH 603 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 105 THROUGH 124 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 125 THROUGH 154 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 155 THROUGH 174 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 175 THROUGH 204 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 205 THROUGH 214 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 215 THROUGH 234 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 235 THROUGH 249 )
25X-RAY DIFFRACTION25CHAIN 'F' AND (RESID 14 THROUGH 23 )
26X-RAY DIFFRACTION26CHAIN 'F' AND (RESID 24 THROUGH 63 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 64 THROUGH 80 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 81 THROUGH 89 )
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESID 90 THROUGH 100 )
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 101 THROUGH 117 )
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESID 48 THROUGH 89 )
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESID 90 THROUGH 107 )
33X-RAY DIFFRACTION33CHAIN 'G' AND (RESID 108 THROUGH 114 )
34X-RAY DIFFRACTION34CHAIN 'G' AND (RESID 115 THROUGH 166 )
35X-RAY DIFFRACTION35CHAIN 'G' AND (RESID 167 THROUGH 244 )
36X-RAY DIFFRACTION36CHAIN 'H' AND (RESID 557 THROUGH 559 )
37X-RAY DIFFRACTION37CHAIN 'H' AND (RESID 563 THROUGH 579 )
38X-RAY DIFFRACTION38CHAIN 'H' AND (RESID 580 THROUGH 603 )

+
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