[English] 日本語
Yorodumi
- PDB-4l1u: Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l1u
TitleCrystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide
Components
  • RNA polymerase-associated protein RTF1 homolog
  • Transcription elongation factor SPT5
KeywordsTranscription/Peptide / Tutor / Plus3 / Peptide binding protein / Spt5 CTR binding / Transcription / Paf1 complex / Rtf1 / ORF association region / Chromatin / Transcription-Peptide complex
Function / homology
Function and homology information


blastocyst growth / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / endodermal cell fate commitment / DSIF complex / regulation of transcription elongation by RNA polymerase II / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / stem cell population maintenance ...blastocyst growth / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / endodermal cell fate commitment / DSIF complex / regulation of transcription elongation by RNA polymerase II / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of DNA-templated transcription, elongation / transcription elongation-coupled chromatin remodeling / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / Wnt signaling pathway / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / protein heterodimerization activity / mRNA binding / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Spt5, KOW domain repeat 6 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote ...Plus-3 domain / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Spt5, KOW domain repeat 6 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Cathepsin B; Chain A / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT5 / RNA polymerase-associated protein RTF1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.424 Å
AuthorsWier, A.D. / Heroux, A. / VanDemark, A.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin.
Authors: Wier, A.D. / Mayekar, M.K. / Heroux, A. / Arndt, K.M. / Vandemark, A.P.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase-associated protein RTF1 homolog
B: RNA polymerase-associated protein RTF1 homolog
C: RNA polymerase-associated protein RTF1 homolog
D: RNA polymerase-associated protein RTF1 homolog
E: RNA polymerase-associated protein RTF1 homolog
F: RNA polymerase-associated protein RTF1 homolog
G: Transcription elongation factor SPT5
H: Transcription elongation factor SPT5
I: Transcription elongation factor SPT5
J: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56243
Polymers101,40810
Non-polymers3,15433
Water1,892105
1
B: RNA polymerase-associated protein RTF1 homolog
G: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0649
Polymers17,3922
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-83 kcal/mol
Surface area8470 Å2
MethodPISA
2
C: RNA polymerase-associated protein RTF1 homolog
H: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8687
Polymers17,3922
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-40 kcal/mol
Surface area8490 Å2
MethodPISA
3
E: RNA polymerase-associated protein RTF1 homolog
I: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8727
Polymers17,3922
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-74 kcal/mol
Surface area8170 Å2
MethodPISA
4
F: RNA polymerase-associated protein RTF1 homolog
J: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7726
Polymers17,3922
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-43 kcal/mol
Surface area8320 Å2
MethodPISA
5
A: RNA polymerase-associated protein RTF1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3015
Polymers15,9201
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: RNA polymerase-associated protein RTF1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6859
Polymers15,9201
Non-polymers7658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.932, 172.514, 58.476
Angle α, β, γ (deg.)90.000, 107.000, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
RNA polymerase-associated protein RTF1 homolog


Mass: 15920.326 Da / Num. of mol.: 6 / Fragment: Plus3, UNP residues 353-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0252, RTF1 / Plasmid: pLC3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+RILP / References: UniProt: Q92541
#2: Protein/peptide
Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 1471.469 Da / Num. of mol.: 4 / Fragment: CTR, UNP residues 778-790 / Source method: obtained synthetically / Details: This sequence occurs naturally in human Spt5 / Source: (synth.) Homo sapiens (human) / References: UniProt: O00267
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.424→50 Å / Num. obs: 40281 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Χ2: 0.665 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.424-2.523.40.37640100.53199.9
2.52-2.623.60.32339920.498199.9
2.62-2.743.40.24840180.533199.9
2.74-2.883.70.18340400.5761100
2.88-3.063.50.12940270.6251100
3.06-3.33.60.08639970.808199.9
3.3-3.633.60.05540350.8831100
3.63-4.153.60.04440360.6891100
4.15-5.233.70.04240440.6981100
5.23-503.60.05940820.794199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.42 Å46.92 Å
Translation2.42 Å46.92 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L1P

4l1p


Resolution: 2.424→46.923 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8414 / SU ML: 0.28 / σ(F): 1.38 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 1750 4.94 %
Rwork0.1777 --
obs0.1801 40278 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.25 Å2 / Biso mean: 55.4372 Å2 / Biso min: 21.54 Å2
Refinement stepCycle: LAST / Resolution: 2.424→46.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 169 105 6993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096985
X-RAY DIFFRACTIONf_angle_d1.1169391
X-RAY DIFFRACTIONf_chiral_restr0.068997
X-RAY DIFFRACTIONf_plane_restr0.0041170
X-RAY DIFFRACTIONf_dihedral_angle_d17.8672611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.424-2.48510.2951400.22652565270594
2.4851-2.55230.2721330.216927662899100
2.5523-2.62740.3081460.217427322878100
2.6274-2.71220.27591430.212927202863100
2.7122-2.80910.25741340.213827572891100
2.8091-2.92160.26121530.22127362889100
2.9216-3.05450.27221350.206827452880100
3.0545-3.21550.26611520.196627272879100
3.2155-3.41690.22381440.182527572901100
3.4169-3.68070.20721360.166827502886100
3.6807-4.05090.23261310.158527422873100
4.0509-4.63660.16761390.130327612900100
4.6366-5.83990.19651780.15827262904100
5.8399-46.9230.21871260.184728042930100
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)
15.04830.7881.1791.88320.71345.57990.0292-1.481.02021.4321-0.387-0.9551-1.18030.02730.04770.6321-0.1013-0.13090.5793-0.02150.7028275.7874-0.049179.2185
24.98240.71610.20954.32071.12280.25520.7264-1.7814-0.63431.2204-0.3623-0.37140.1082-0.174-0.11360.394-0.0635-0.02350.5140.09580.3524265.3339-9.401578.2365
32.5676-2.6430.52425.1452-2.6341.82640.0105-0.35870.21440.28650.33370.5694-0.4451-0.028-0.35540.3325-0.0233-0.03350.35720.05950.4697249.9511-10.86271.6449
48.82730.53580.72120.41330.20955.61460.0398-0.28350.4187-0.50080.44-0.4313-0.90780.5903-0.27360.2931-0.0013-0.00590.30080.09670.3591255.8236-3.146569.0058
56.5499-0.17690.64346.8011-1.37945.5321-0.47130.6968-0.7775-0.42190.4673-0.44430.04350.16610.02940.2548-0.10940.08790.4209-0.04920.3648263.9895-13.466165.4827
66.24472.61810.30758.0271-1.89856.2503-0.43880.59870.0883-1.05120.19930.15420.48760.1150.19460.3658-0.14710.00870.5372-0.00260.3972248.8302-18.038359.9895
72.19062.09580.48115.0443-1.47623.2005-0.27061.49890.2539-0.41110.71870.4456-0.45780.3042-0.38740.4105-0.15070.02540.5088-0.0210.3232256.3028-11.633462.1219
88.59173.95782.72373.21330.96720.9242-0.13322.0793-0.617-0.53090.0316-0.42510.62940.74520.08230.4401-0.28160.0431.1619-0.01250.2667266.7806-10.83559.146
99.54263.9218-0.53413.7274-0.99370.6556-0.15550.2467-1.062-0.18680.0102-0.67120.0950.22630.10810.2772-0.0251-0.00780.3290.00240.4037269.7808-13.940770.2075
103.5978-3.08440.26745.75843.01373.7481-0.35620.22990.3758-0.08880.25920.3426-0.85060.3660.19850.2862-0.0834-0.00390.4105-0.02250.3522274.4072-0.548368.8842
112.18341.33880.71073.95750.67025.39880.8597-0.37741.39870.2825-0.11730.6592-0.0375-0.7234-0.78090.5506-0.05590.12760.6190.00550.4564259.86420.348878.6355
123.1505-0.9865-0.33615.7369-1.98375.15080.40030.73480.5894-0.5445-0.07340.7132-0.6883-0.3094-0.26160.4790.08920.05760.42040.08560.4782231.102210.589661.4946
135.0011-0.38270.77515.8116-1.67092.92550.01990.2999-0.5601-1.03010.1580.16820.3331-0.0876-0.18240.3612-0.0470.00320.2908-0.06190.316229.9571-7.945368.0584
145.1242-3.22030.63043.0954-1.71015.325-0.1484-0.5567-0.10090.0002-0.0008-1.5272-0.22760.60450.00520.2488-0.02970.01030.52050.03420.3775238.3975-5.77574.2331
152.0144-0.8466-0.99511.362-0.42943.834-0.0539-0.3203-0.02180.3712-0.29570.8647-0.4299-0.64940.12330.36810.06990.13120.4376-0.130.7079216.36111.377872.8452
162.35480.80732.92875.7529-0.02256.08920.3068-0.91640.78740.2711-0.17380.0458-0.4028-0.1751-0.18860.2895-0.02960.10030.3512-0.00930.2986224.41171.319175.2976
173.56852.54213.03064.58644.73365.02550.6607-0.546-0.5492-0.22740.4203-0.653-0.49820.577-1.09640.4491-0.1424-0.00290.4060.00390.4152225.3876-13.451781.7941
183.1760.33151.33315.5113-0.81674.87530.211-0.13760.05550.3066-0.15630.0866-0.42580.00630.00450.29870.01960.03960.3077-0.06890.2653225.3811-1.707576.3249
190.9088-0.1205-0.76488.38661.41721.05040.02770.02260.57710.3772-0.23380.6276-0.2108-0.05410.23970.5262-0.0050.11090.29390.02830.3669225.104114.510469.7268
204.9112-5.0990.11875.3614-1.22988.55010.80890.12860.3419-1.4701-0.3433-0.7177-0.02390.3585-0.35840.39920.04240.06130.3266-0.01070.4243240.44563.118863.237
212.14560.08220.38614.43741.21382.4260.1427-0.01090.0635-0.0316-0.1838-0.00020.1865-0.19370.04620.2465-0.0432-0.00810.28370.00680.2611244.7786-35.023571.2057
223.9246-1.123-1.71157.55392.77264.60040.1584-0.3290.04510.30640.0733-0.37940.3250.0948-0.23770.26-0.041-0.07180.34940.03130.3275248.4786-35.172376.0402
232.24310.26880.93894.6054-1.66782.9320.2088-0.3245-0.42790.2676-0.0939-1.0365-0.21420.0612-0.02460.5847-0.0247-0.12120.2934-0.030.5981249.5419-50.93968.7492
247.3276-3.9533-1.23673.05173.14056.76710.7516-0.2040.1119-0.7579-0.23910.4463-0.2458-0.2734-0.47540.4654-0.0137-0.05160.30240.040.4714233.8177-39.590662.6019
255.32551.4661-2.67322.44830.27971.87710.1848-0.76270.03080.1281-0.15320.13690.17590.0338-0.03190.3497-0.0427-0.03870.4279-0.0530.2259210.3868-27.588876.7355
268.34-1.956-0.46771.36270.98612.70460.0784-0.2092-0.4771-0.26320.0005-0.19440.51970.2639-0.04520.36030.0142-0.0850.3123-0.08710.4333222.1394-32.398168.8805
276.39141.316-2.22697.03792.68794.5810.35730.15041.5251-1.1339-0.010.9238-0.6658-0.6848-0.21620.4189-0.0264-0.11050.52210.02410.5952206.4529-15.562865.6657
288.3099-3.0926-0.93622.82893.04016.0076-0.24030.26520.3641-0.27250.652-0.03180.0813-0.485-0.36080.3355-0.06640.0030.39970.06030.2682210.0799-22.986964.6199
297.5257-0.0465-1.16667.897-0.80898.0328-0.5041.45760.9544-1.14560.0692-1.1218-0.0729-0.53960.11940.4148-0.09590.07770.65-0.05920.5534225.2479-18.534659.5624
302.89090.251-0.37184.81830.42633.7664-0.16831.83980.5613-0.55990.7299-0.43840.2654-0.0908-0.35970.4545-0.13580.04540.5514-0.07970.3276217.7159-25.007761.856
317.37014.4086-2.24973.1064-1.43030.7268-0.61120.08390.1403-0.74510.50080.15850.6611-1.31050.02740.5276-0.35230.03630.84850.13090.2022207.2352-25.966159.0476
322.71731.4642-0.08847.15581.66572.89540.19410.29511.29510.05790.22150.0670.1043-0.0769-0.29740.25440.0131-0.07860.3345-0.05490.3225213.0217-18.325869.657
337.93615.16981.8999.88473.75153.60550.15160.23471.06270.5079-0.230.88110.0773-0.00070.13580.3019-0.09150.0370.34820.02750.3487197.0899-25.380770.3088
342.3787-3.05873.00434.796-3.91183.63890.04130.1163-0.999-0.138-0.13250.25360.54120.09540.040.347-0.121-0.02340.6774-0.04860.3189199.5196-35.56869.2005
352.15423.35280.51826.17150.99242.01710.6333-1.0328-0.52370.8759-0.6421-0.5080.6010.9189-0.00180.4986-0.0013-0.0270.6620.10590.3402214.818-36.536678.9889
365.3940.23062.4592.8012-1.13152.00370.1443-1.421-1.0778-0.00390.42860.3496-0.0987-0.3389-0.49430.4759-0.03640.10870.47870.07180.329239.60571.224452.1561
373.7484-2.841-0.06166.41310.30034.0179-0.556-0.31770.72720.2840.2752-0.0391-0.7250.04330.21440.5334-0.0105-0.03910.3377-0.02440.4682233.535619.378243.6496
386.0661-0.9347-1.34194.9484-1.54524.46280.05490.4601-0.9074-0.240.09080.1875-0.0727-0.0877-0.15250.36020.02520.05270.3279-0.10730.3339231.97036.280934.721
394.1242-2.9242-1.06087.2721.0553.93950.25020.2591-0.0192-0.7939-0.38830.5337-0.60580.09530.16650.4507-0.0029-0.04530.3402-0.02310.3115232.200414.010434.2377
402.1898-1.5224-0.97873.85841.03133.68540.1340.5748-0.80950.44430.01910.4660.3075-0.2134-0.2450.3331-0.004-0.01270.3175-0.00920.4742238.9506-3.672940.7689
413.7757-1.4835-0.64275.25033.03776.899-0.2459-0.2070.14730.37630.5148-0.2996-0.16020.8094-0.23790.3762-0.04590.06660.3853-0.02250.3568242.769.072450.7659
422.8981-1.2157-1.28698.18262.25143.0003-0.3453-0.1935-0.20510.34360.3569-0.27870.4340.1473-0.07030.39850.0275-0.03880.37460.06170.3047238.3442-49.006645.7999
436.49890.2989-0.26744.0612.09282.9052-0.06230.60270.6461-0.53810.2208-0.6137-0.1099-0.0951-0.20460.44710.10560.01360.47090.11120.366241.6215-42.094833.8031
446.7985-3.2150.46076.36422.72741.9401-0.05610.9511-0.3995-0.9951-1.2436-0.29150.09860.11680.59890.62960.06780.1080.43530.22940.7661245.859-58.791529.0913
453.2472-2.3970.23826.45690.93894.28830.05290.59650.1206-0.5001-0.2656-0.47010.52650.02180.25060.48140.01860.11460.45630.05160.3797240.2382-48.161934.1273
462.1167-2.3710.06445.6628-1.61682.86370.37380.84571.00280.27360.0683-0.4359-0.37870.0171-0.10160.37680.10520.08580.39180.05310.4848235.0839-32.478840.1717
474.2712-3.85582.19383.3953-3.1495.6489-0.2133-0.39950.0432-0.01070.17930.12570.2811-0.41430.08390.4509-0.0258-0.0880.44890.04040.3885231.5286-45.379150.0008
482.08150.0186-0.29247.0272-1.8186.32090.3162-0.17260.20930.3771-0.32820.4612-0.001-0.8235-0.12690.4146-0.00940.04580.5064-0.04020.5552216.2995-6.827372.5796
492.21970.42530.477.37733.2663.6525-0.0373-1.02050.36670.3388-0.1033-1.1861-1.30451.01070.24570.42-0.1336-0.08130.6212-0.08080.5933258.3094-30.130673.6054
501.67292.18951.44538.2284-0.29322.17170.88730.53040.7871-0.00120.7568-0.1038-1.1834-1.509-1.45470.7210.04010.01180.82650.14330.8762223.80718.995133.0444
515.395-0.4402-2.62552.19841.78488.70981.1486-0.92070.7768-1.8953-1.0075-0.78570.71971.64540.26190.9650.05080.23390.88510.01570.8449252.3241-44.962833.3636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 349 through 355 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 356 through 365 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 366 through 377 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 385 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 386 through 410 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 411 through 419 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 420 through 430 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 431 through 437 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 438 through 461 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 462 through 468 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 469 through 483 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 350 through 362 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 363 through 372 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 373 through 385 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 386 through 396 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 397 through 410 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 411 through 419 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 420 through 448 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 449 through 468 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 469 through 483 )B0
21X-RAY DIFFRACTION21chain 'C' and (resid 350 through 419 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 420 through 448 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 449 through 468 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 469 through 483 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 349 through 372 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 373 through 385 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 386 through 396 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 397 through 410 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 411 through 419 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 420 through 430 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 431 through 437 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 438 through 448 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 449 through 461 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 462 through 468 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 469 through 484 )D0
36X-RAY DIFFRACTION36chain 'E' and (resid 349 through 362 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 363 through 385 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 386 through 410 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 411 through 448 )E0
40X-RAY DIFFRACTION40chain 'E' and (resid 449 through 461 )E0
41X-RAY DIFFRACTION41chain 'E' and (resid 462 through 482 )E0
42X-RAY DIFFRACTION42chain 'F' and (resid 349 through 385 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 386 through 410 )F0
44X-RAY DIFFRACTION44chain 'F' and (resid 411 through 419 )F0
45X-RAY DIFFRACTION45chain 'F' and (resid 420 through 448 )F0
46X-RAY DIFFRACTION46chain 'F' and (resid 449 through 461 )F0
47X-RAY DIFFRACTION47chain 'F' and (resid 462 through 482 )F0
48X-RAY DIFFRACTION48chain 'G' and (resid 781 through 788 )G0
49X-RAY DIFFRACTION49chain 'H' and (resid 780 through 790 )H0
50X-RAY DIFFRACTION50chain 'I' and (resid 783 through 787 )I0
51X-RAY DIFFRACTION51chain 'J' and (resid 782 through 786 )J0

+
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