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- PDB-4pc1: Elongation Factor Tu:Ts complex with a bound phosphate -

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Basic information

Entry
Database: PDB / ID: 4pc1
TitleElongation Factor Tu:Ts complex with a bound phosphate
Components(Elongation factor ...) x 2
KeywordsTRANSLATION / G:GEF complex / elongation factor / Protein synthesis
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 ...GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 / Tetrahydropterin Synthase; Chain A / Ubiquitin-associated (UBA) domain / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / UBA-like superfamily / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEAD (II) ION / PHOSPHATE ION / Elongation factor Tu / : / Elongation factor Ts
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsThirup, S.S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.
Authors: Thirup, S.S. / Van, L.B. / Nielsen, T.K. / Knudsen, C.R.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
B: Elongation factor Tu
C: Elongation factor Ts
D: Elongation factor Ts
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,34912
Polymers147,3474
Non-polymers1,0038
Water25,2571402
1
A: Elongation factor Tu
C: Elongation factor Ts
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4898
Polymers73,6732
Non-polymers8166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-32 kcal/mol
Surface area29900 Å2
MethodPISA
2
B: Elongation factor Tu
D: Elongation factor Ts
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8604
Polymers73,6732
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-33 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.510, 109.770, 195.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Elongation factor ... , 2 types, 4 molecules ABCD

#1: Protein Elongation factor Tu / EF-Tu


Mass: 43340.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: tufA, tuf, ECDH10B_3514 / Production host: Escherichia coli (E. coli) / References: UniProt: B1X6I9, UniProt: A0A0M3KKV1*PLUS
#2: Protein Elongation factor Ts / EF-Ts


Mass: 30332.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tsf, BN17_45931, ECs0172, LF82_2325 / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPM7

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Non-polymers , 5 types, 1410 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pb
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1402 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Hepes,22% PEG 6000, 150mM NaCl, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9215 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9215 Å / Relative weight: 1
ReflectionResolution: 1.95→68.8 Å / Num. obs: 118029 / % possible obs: 96.8 % / Redundancy: 2.7 % / Rsym value: 0.091 / Net I/σ(I): 11.6
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.8 / % possible all: 97.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementStarting model: PDB ENTRY 1TUI
Resolution: 1.95→68.786 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 4526 3.99 %Random
Rwork0.1743 ---
obs0.1757 113382 98.08 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→68.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9788 0 38 1402 11228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310073
X-RAY DIFFRACTIONf_angle_d1.3513601
X-RAY DIFFRACTIONf_dihedral_angle_d13.8883799
X-RAY DIFFRACTIONf_chiral_restr0.0541559
X-RAY DIFFRACTIONf_plane_restr0.0071775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.32151320.27793625X-RAY DIFFRACTION98
1.9722-1.99540.29141390.2583581X-RAY DIFFRACTION98
1.9954-2.01970.2951620.25153555X-RAY DIFFRACTION98
2.0197-2.04530.28481520.24043571X-RAY DIFFRACTION97
2.0453-2.07220.23931310.23253597X-RAY DIFFRACTION98
2.0722-2.10060.28141350.21743610X-RAY DIFFRACTION97
2.1006-2.13060.27371690.21753557X-RAY DIFFRACTION98
2.1306-2.16240.22931510.20513608X-RAY DIFFRACTION97
2.1624-2.19620.21911640.20223573X-RAY DIFFRACTION99
2.1962-2.23220.22881560.19173556X-RAY DIFFRACTION98
2.2322-2.27070.21141410.1863612X-RAY DIFFRACTION99
2.2707-2.3120.22821550.18553605X-RAY DIFFRACTION98
2.312-2.35640.24141580.17873605X-RAY DIFFRACTION98
2.3564-2.40450.2041430.17693574X-RAY DIFFRACTION98
2.4045-2.45680.23451610.17713587X-RAY DIFFRACTION97
2.4568-2.5140.24611530.17173607X-RAY DIFFRACTION98
2.514-2.57690.20411660.16953582X-RAY DIFFRACTION98
2.5769-2.64650.23811580.17373588X-RAY DIFFRACTION97
2.6465-2.72440.20831380.16883593X-RAY DIFFRACTION97
2.7244-2.81230.20631350.17223647X-RAY DIFFRACTION98
2.8123-2.91290.21691650.17373587X-RAY DIFFRACTION98
2.9129-3.02950.19881520.16533594X-RAY DIFFRACTION98
3.0295-3.16740.19561400.1723640X-RAY DIFFRACTION97
3.1674-3.33440.17971590.1633588X-RAY DIFFRACTION97
3.3344-3.54330.17541600.16493622X-RAY DIFFRACTION98
3.5433-3.81680.21111310.15743725X-RAY DIFFRACTION99
3.8168-4.20090.17541490.14213731X-RAY DIFFRACTION99
4.2009-4.80860.15431450.13253774X-RAY DIFFRACTION100
4.8086-6.05780.18481530.15593825X-RAY DIFFRACTION100
6.0578-68.82890.18271730.17373937X-RAY DIFFRACTION99
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)
11.89330.67280.35822.39660.61482.28870.0625-0.16070.11560.18030.0282-0.1942-0.15790.0587-0.02450.18440.0121-0.01240.1224-0.0280.147414.400161.42773.3049
23.9769-1.77672.52073.2745-2.88623.6289-0.1916-0.10620.07510.39040.1319-0.5235-0.34970.32860.11510.39620.1516-0.11840.5264-0.1840.304133.11845.4271101.8355
30.19760.09710.0070.92230.64171.8738-0.1685-0.40470.15910.19990.00570.0445-0.1401-0.3043-0.06320.25990.1264-0.05270.4402-0.17880.231226.978935.925693.1835
42.44920.6765-0.88112.0915-0.24921.50170.1649-0.3336-0.28740.2398-0.18010.06030.1918-0.0487-0.0250.3166-0.1129-0.03230.21890.0520.170748.1919-16.682779.5634
50.07970.0110.16440.9855-0.35640.40940.0989-0.0835-0.20950.43130.19150.2847-0.0166-0.21730.38350.5918-0.39540.331.13950.1606-0.023323.9194-2.000199.2845
60.4288-0.2423-0.03730.23290.07440.04510.1159-0.635-0.37530.3720.10370.32370.0035-0.08640.14840.8629-0.55190.30381.3120.1458-0.050920.48383.5433105.7804
71.1993-0.0734-0.09711.7153-0.05781.34030.1976-0.6799-0.14860.6319-0.29280.00640.1532-0.2328-0.03430.3173-0.16280.02940.5001-0.01710.107732.474811.13791.551
84.4766-0.28961.19412.0215-0.44243.1691-0.086-0.4345-0.06430.10740.26310.2533-0.1426-0.5394-0.15770.18730.0871-0.00820.25280.04090.1844-6.997962.963957.9131
93.5689-3.7578-0.71844.52640.50041.75430.1379-0.0496-0.2282-0.09370.04960.2771-0.0526-0.2207-0.09620.1556-0.0076-0.02290.1320.04710.1408-1.071856.419349.0393
100.25330.26640.04122.9856-0.06430.2992-0.01-0.00450.02430.09850.02360.06250.0188-0.0756-0.02040.09450.0032-0.01220.12470.00030.13656.982335.542356.0536
110.5438-0.71210.32774.0864-0.67310.7032-0.0326-0.02050.0199-0.11350.07490.0059-0.0153-0.024-0.05510.0709-0.01740.00890.1179-0.00210.1028.34332.956554.4032
123.04260.7927-1.77412.8062-0.23095.06140.03390.1411-0.18810.08320.02670.00550.1009-0.0693-0.02190.08810.0107-0.04540.1037-0.01530.14519.346817.131159.5392
134.04474.0934.36515.52224.42625.8272-0.21080.38350.1922-0.2758-0.12350.1813-0.2415-0.07930.25610.1570.0430.00560.21140.0170.136842.453918.851447.5774
146.02951.1947-0.22973.5716-2.11451.58280.08350.31-0.3951-0.1887-0.1028-0.07050.19860.03690.06860.18270.0228-0.03440.1798-0.06350.151743.245513.224653.4875
152.08670.1660.63532.3725-0.29672.02070.0917-0.0392-0.27830.0306-0.102-0.13440.25620.0661-0.00710.0934-0.0045-0.02130.1101-0.01070.152920.312613.577961.9598
160.9320.91921.04581.45081.93822.5262-0.0670.11460.0098-0.45820.4524-0.9411-0.30410.4725-0.29240.2626-0.01410.1310.255-0.08230.480226.242752.945860.4766
173.0343-2.24620.38813.45020.25153.57690.0247-0.184-0.64040.1256-0.0698-0.63850.70320.5185-0.04760.37140.0661-0.05850.25870.09460.525272.9692-21.000371.8312
181.13810.2458-0.1261.8857-0.02760.9023-0.0309-0.0883-0.0360.1438-0.001-0.09960.13110.05470.00420.15590.00040.00090.1395-0.00520.117965.20482.954865.7232
191.085-0.4642-0.29832.55870.7351.0928-0.0881-0.09950.09960.0240.0978-0.13850.05770.0131-0.00990.1029-0.0154-0.03210.1225-0.01780.108962.434911.593464.6273
203.60650.41612.04270.39050.18562.0601-0.14290.21910.5488-0.0501-0.1188-0.0575-0.13480.08510.21030.17160.02720.00390.11820.01290.266543.327927.304456.9689
212.84140.71333.37123.57511.54225.06630.03390.33150.6379-0.2758-0.1849-0.1847-0.19390.25120.14420.16430.02580.03920.16120.02070.248230.295732.013951.1531
220.40890.3563-0.43151.2380.02321.78050.0635-0.06590.48170.0197-0.07260.1571-0.2938-0.11690.0490.15580.0023-0.02220.1433-0.05220.328649.162631.041267.3208
233.28492.1697-1.91511.6027-1.66051.814-0.44010.2522-0.1131-1.01180.51680.35150.3868-0.428-0.1330.3624-0.0725-0.14620.28130.05370.272242.5393-5.53263.9357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 8:198)
2X-RAY DIFFRACTION2chain 'A' and (resseq 199:230)
3X-RAY DIFFRACTION3chain 'A' and (resseq 231:393)
4X-RAY DIFFRACTION4chain 'B' and (resseq 8:197)
5X-RAY DIFFRACTION5chain 'B' and (resseq 198:223)
6X-RAY DIFFRACTION6chain 'B' and (resseq 224:260)
7X-RAY DIFFRACTION7chain 'B' and (resseq 261:393)
8X-RAY DIFFRACTION8chain 'C' and (resseq 1:32)
9X-RAY DIFFRACTION9chain 'C' and (resseq 33:51)
10X-RAY DIFFRACTION10chain 'C' and (resseq 52:106)
11X-RAY DIFFRACTION11chain 'C' and (resseq 107:161)
12X-RAY DIFFRACTION12chain 'C' and (resseq 162:186)
13X-RAY DIFFRACTION13chain 'C' and (resseq 187:204)
14X-RAY DIFFRACTION14chain 'C' and (resseq 205:225)
15X-RAY DIFFRACTION15chain 'C' and (resseq 226:259)
16X-RAY DIFFRACTION16chain 'C' and (resseq 260:280)
17X-RAY DIFFRACTION17chain 'D' and (resseq 2:32)
18X-RAY DIFFRACTION18chain 'D' and (resseq 33:106)
19X-RAY DIFFRACTION19chain 'D' and (resseq 107:161)
20X-RAY DIFFRACTION20chain 'D' and (resseq 162:204)
21X-RAY DIFFRACTION21chain 'D' and (resseq 205:225)
22X-RAY DIFFRACTION22chain 'D' and (resseq 226:259)
23X-RAY DIFFRACTION23chain 'D' and (resseq 260:279)

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