4PC1

Elongation Factor Tu:Ts complex with a bound phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.

Thirup, S.S.Van, L.B.Nielsen, T.K.Knudsen, C.R.

(2015) J Struct Biol 191: 10-21

  • DOI: 10.1016/j.jsb.2015.06.011
  • Primary Citation of Related Structures:  
    4PC7, 4PC1, 4PC2, 4PC3, 4PC6

  • PubMed Abstract: 
  • Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks ...

    Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.


    Organizational Affiliation

    Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor TuA, B394Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: tufAtufECDH10B_3514
UniProt
Find proteins for A0A0M3KKV1 (Escherichia coli (strain K12 / DH10B))
Explore A0A0M3KKV1 
Go to UniProtKB:  A0A0M3KKV1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor TsC, D282Escherichia coliMutation(s): 0 
Gene Names: 
tsfBN17_45931ECs0172LF82_2325A6581_19555A6592_02980A6V01_15335A8C65_17845A9P13_21170A9R57_04405A9X72_20400AAW05_12810AC067_04640AC789_1c01680ACN002_0175ACN68_08305ACN81_28530ACU57_18570AJ318_03075AM270_18165AM446_22750AM464_17650AM465_25880AMK83_01985AML07_22930APT94_20000APU18_02560APZ14_11105ARC77_20185AU473_25965AUQ13_07495AUS26_23150AW059_09845AW106_08760AWB10_21010AWE53_010745AWF59_003775AWG78_007090AWG90_002350AWP75_13490AZZ83_003981B6V57_00935B7C53_01355B9M99_16260B9N33_22510B9T59_07515BANRA_00548BANRA_00643BANRA_02272BANRA_03340BB545_20905BE963_14840BEN53_03090BER14_07775BFD68_21810BHF03_16555BHF46_07880BHS81_00655BHS87_00810BIQ87_00800BIU72_13400BIZ41_19070BJJ90_21355BK248_07250BK292_13675BK296_02525BK334_15015BK373_09600BK375_04640BK383_20235BMA87_12310BMT49_02180BMT91_01360BOH76_17710BON63_15440BON65_09435BON66_02945BON69_16400BON71_14875BON72_09385BON75_17155BON76_15475BON83_24845BON86_04415BON87_26685BON91_06955BON92_02760BON94_19470BON95_13025BON96_17205BON98_18175BTQ04_14415BTQ06_06495BUE81_01700BvCms2454_04106BvCms28BK_01214BvCms35BK_02144BvCmsC61A_04365BvCmsHHP001_04839BvCmsHHP019_00043BvCmsHHP056_04093BvCmsKKP036_03787BvCmsKKP061_01634BvCmsKSNP073_05555BvCmsKSNP081_02654BvCmsKSNP120_00103BvCmsKSP011_02197BvCmsKSP024_03110BvCmsKSP026_04710BvCmsKSP045_01849BvCmsKSP058_03766BvCmsKSP067_02025BvCmsNSNP036_02488BvCmsNSP006_04060BvCmsNSP007_03763BvCmsNSP047_03381BvCmsNSP072_03669BvCmsOUP014_04096BvCmsSINP011_04062BvCmsSINP022_00327BvCmsSIP019_04899BvCmsSIP044_04942BVL39_02180BW690_02460BWI89_14045BWP17_11905BXT93_00715BZL31_14930BZL69_20195C2M16_10805C4K41_20905C4M78_19965C5715_17340C5F72_21615C5F73_07965C5N07_08585C5P01_08930C5P44_18005C6669_04240C6B13_04320C7235_20225C7B02_09150C7B06_05870C7B07_04270C7B08_09685C7B18_05295C9098_16105C9114_07020C9141_10725C9160_13580C9162_08280C9201_10245C9306_11350C9E25_15395C9E67_25200C9Z03_02470C9Z23_08410C9Z28_18080C9Z29_10370C9Z37_18005C9Z39_04995C9Z43_09530C9Z68_04790C9Z69_04815C9Z70_08110C9Z78_00160C9Z78_02780C9Z89_09385CA593_02860CCZ14_20500CCZ17_20475CDC27_24695CDL37_07250CF006_21200CG692_09490CI641_016490CI693_15100CI694_28170CIG45_06980CJU63_00910CJU64_00880CMR93_22850CO706_23060COD30_14760COD46_06640CQP61_22085CR538_20635CR539_04940CRD98_15330CRE06_00160CRJUMX01_610032CRM83_15085CRT43_00995CRX46_05010CSB64_09590CT146_12110CUB99_08010CV83915_01405CVH05_24465CWM24_05045CWS33_09625D0X26_09410D2184_08590D2185_20135D2188_12790D3821_06215D3822_17330D3C88_01895D3M98_08930D3O91_03195D3P01_06960D3P02_17580D3Y67_16410D4011_00160D4023_14645D4074_16635D4628_06785D4636_06390D4638_01775D4660_00160D4718_00160D4L91_00160D4M06_01440D4U49_05945D4U85_02325D4V08_16075D5H35_10985D5I97_00160D6004_09735D6C36_00165D6D43_00160D6T60_04045D6T98_04160D6W00_07905D6X36_11840D6X63_10630D6X76_09795D7K33_03405D7K63_00160D7K66_11605D7W70_19200D7Y10_00160D7Z75_07415D8Y65_01900D9610_09460D9C99_12685D9D20_18635D9D31_08890D9D33_03380D9D43_02300D9D44_06775D9D94_08700D9E13_16325D9E19_12690D9E34_01100D9E35_14525D9E49_02140D9E73_02480D9F17_00160D9F32_01780D9F87_17235D9G11_19095D9G29_09880D9G42_07580D9G48_08790D9G69_05825D9G95_20565D9H10_00160D9H36_21795D9H53_14250D9H68_13780D9H70_04350D9H94_14040D9I18_14965D9I20_08110D9I87_01635D9I88_06430D9J03_00160D9J11_16830D9J44_14075D9J46_02890D9J52_04555D9J58_13450D9J60_02070D9J63_20110D9J78_12375D9K02_06615D9K48_09970D9K54_16755D9L89_00160D9L99_05935D9X77_14910D9X97_00160D9Z28_03945DAH18_22170DAH26_11205DAH30_10605DAH32_15115DAH34_04180DAH37_16325DAH43_04035DB359_12950DBQ99_21350DD762_01100DEN86_04060DEN89_20290DEN97_04420DEO04_22095DEO19_04205DEO20_19725DIV22_06275DJ487_06015DJ492_12765DK132_00120DL251_18755DL257_01635DL292_03075DL326_07515DL455_01605DL479_13350DL530_05565DL545_20385DL705_11955DL979_07565DLT82_10655DLU50_09125DLU67_09925DLU82_13740DLW60_08640DLW88_03745DLX38_05605DLX40_11055DLY41_15715DLY44_08775DM102_18375DM129_14545DM155_08215DM272_00160DM280_04670DM296_03660DM382_13440DM820_06520DM962_03235DM973_00120DMC44_08860DMI04_00160DMI53_01505DMO02_00160DMY83_01560DMZ50_04120DN627_10240DN660_06395DN700_05170DN703_10115DN808_03370DNB37_01425DNC98_14255DND16_04805DND79_05995DNI21_01660DNJ62_00160DNK12_00160DNQ45_10110DNR35_01440DNR41_13195DNW42_10165DNX19_10630DNX30_02265DOE35_00160DOM23_00160DOS18_01645DOT81_00160DOU81_00160DOY22_00160DOY56_00160DOY61_10500DOY67_01860DP258_09350DP265_12815DP277_13720DQE91_03220DQF36_13640DQF57_05660DQF71_09505DQF72_13125DQG35_00160DQO13_06245DQP61_02345DRP48_00160DRW19_04920DS143_09095DS721_00160DS732_05780DS966_12900DT034_05330DTL43_05915DTL90_09740DTM10_02790DTM45_12640DTZ20_16570DU309_06135DU321_03655DU333_05945DVB38_09160DW236_10620DWB25_20300DXT69_01465DXT71_01915DXX80_017140E0I42_18985E0K84_12850E0L04_16460E0L12_05060E2112_01235E2114_18165E2115_17380E2119_15585E2127_15015E2128_01355E2129_02855E2134_11980E2135_11640E2148_14075E4A44_06405E4K51_05785E4K55_06960E4K59_00160E4K60_12615E4K61_17660E5P22_04095E5P24_16200E5P28_13980E5P37_21195E5S42_18240E5S56_11575E5S58_05600E5S61_20140E5S62_13850EA159_18555EA164_17315EA167_19600EA174_03760EA184_05185EA189_12740EA191_19900EA198_08650EA200_20620EA203_17925EA213_17810EA214_17050EA218_05090EA222_15555EA223_13385EA225_05605EA231_02015EA232_17980EA233_03705EA235_19380EA239_13415EA242_20410EA245_19670EA247_16765EA250_20390EA410_04880EA429_13725EA433_18615EA434_02540EA435_20375EA834_19140EAI42_08305EAI46_03640EAI52_11010EAM59_13725EAN70_14180EAN77_17420EAX79_05555EB476_18080EB509_04555EB510_04560EB515_00160EB525_RS05100EBA84_00160EBJ06_10270EBM08_06960EC1094V2_3682EC3234A_2c01510EC3426_00921ECONIH1_00895ECTO124_04041ECTO6_03893ED178_08860ED307_13040ED600_04640ED607_02620ED611_09630ED648_00160ED903_08490ED944_00160EEA45_04505EEP23_00160EF082_10770EF173_00160EG075_06610EG599_10025EG796_02795EG808_13605EGC26_04055EGT48_20255EGU87_00160EH186_01430EH412_11885EHD45_00160EHD63_00160EHD79_10730EHH55_16980EHJ36_11750EHJ66_10075EHV81_01730EHV90_15895EHW09_06775EHX09_00160EI021_19850EI028_17530EI032_14685EI041_03155EIA08_06330EIA21_00160EIZ93_07920EJ366_18205EJC75_22735EKI52_10430EL75_3595EL79_3704EL80_3651ELT17_01255ELT20_04475ELT22_08880ELT23_12170ELT33_15865ELT48_12185ELT49_18480ELT58_11820ELU82_16770ELU85_21265ELU96_20280ELV00_10930ELV05_06470ELV08_10275ELV13_13150ELV15_10270ELV22_16460ELV24_19195ELV28_04180ELX56_19480ELX70_19410ELX76_14555ELX79_12485ELX83_20600ELY05_11475ELY23_06760ELY24_11295ELY41_06545ELY48_16910ELY50_16135EO241_11805EPS76_09890EPS91_15140EPS94_12735EPT01_02590EPU41_00955EQ820_08900EQ823_16630EQ825_22915EQ830_01900EQO00_21080ERL57_05900ERS085365_03086ERS085366_02720ERS085374_03831ERS085379_00537ERS085383_01176ERS085404_00707ERS085406_00570ERS085416_03649ERS139211_02986ERS150873_01112ERS150876_00064EST51_20095EVY14_15620EWK56_14890EXM29_15755ExPECSC019_03546ExPECSC038_03989ExPECSC065_04178EXX06_08820EXX13_05320EXX23_14670EXX24_10900EXX53_06970EXX55_08285EXX71_19555EXX78_21210EXX87_03340EYD11_18535EYX82_24370EYX99_20955EYY27_25450EYY34_22880EYY78_09595F1E13_07860F1E19_15480F7F00_13235F7F11_02070F7F18_06635F7F23_12915F7F26_13525F7F29_08170F7G01_02650F7G03_01460F9040_13540F9050_00160F9059_17975F9225_05900F9B07_03515F9Z53_10775FAF34_018070FE846_19740FKO60_12335FNJ67_21460FNJ69_22380FNJ83_02350FORC82_3869FQ022_03090FQ915_10745FQR64_18685FQU83_21880FQZ46_06400FRV13_02395FV293_02890FV295_13975FV438_03740FVB16_04520FWK02_08145FZ043_04030FZC17_23570FZN06_13890FZN26_20730FZN30_04800G3565_18170G3V64_18515G5603_21755G5608_21990G5616_00160G5632_13930G5668_12585G5670_12925G5675_00160G5680_11540G5686_12655G5688_15325G5696_01315G5697_15865GFU40_18980GFU45_18865GFU47_13785GHR40_00585GII67_17715GII91_13050GIY13_04540GIY19_11135GJ638_08090GJD97_22990GKE15_05195GKE16_05180GKE22_02180GKE24_06255GKE26_05195GKE29_08790GKE31_05155GKE39_03925GKE46_02205GKE53_02205GKE58_05110GKE60_05165GKE64_02205GKE69_03510GKE77_05540GKE79_03915GKE87_12055GKE92_14175GKE93_04105GKE98_08640GKF03_12925GKF21_15810GKF28_16150GKF34_15445GKF47_15420GKF52_14730GKF89_14775GKG08_11270GKG09_11870GKG11_12460GKG12_02115GKG22_11880GKG29_11920GN312_14030GNZ00_06520GNZ02_07905GNZ03_07300GNZ05_09820GP650_06520GP654_11810GP661_02975GP662_15450GP664_18010GP666_04995GP671_16640GP678_08075GP689_18800GP698_00160GP700_07635GP711_09535GP712_03550GP720_09580GP727_05965GP892_07450GP912_05755GP935_09855GP945_16375GP946_16435GP950_21255GP979_07880GQA06_13070GQA23_04975GQA63_20860GQA64_21240GQE30_11635GQE33_20290GQE34_08850GQE36_01705GQE47_19145GQE51_01810GQE58_21120GQE68_05065GQE88_09265GQE93_18415GQF59_21020GQL64_13730GQM04_19845GQM09_07095GQM10_19905GQM17_05185GQM28_22095GQN16_14995GQN24_12830GQN33_07390GQS26_13495GQY14_02315GRW05_07700GRW12_02155GRW27_19965GRW30_06960GRW42_18980GRW57_10405GRW80_16645GRW81_09815GUB08_19165GUB85_08140GUB91_10110GUB95_11690GUC01_17885GUC12_11250GUC40_06240GUI16_06120GUI33_00160GZS12_18930HmCms169_00361HmCms184_03910HmCmsJML074_03000HmCmsJML079_04928HmCmsJML146_01753HmCmsJML204_00826HmCmsJML236_01510HMPREF3040_02611HW43_04605MJ49_06190MS6198_01850MS8345_00168NCTC10082_01382NCTC10089_04075NCTC10764_05764NCTC10767_03963NCTC10963_04190NCTC10974_04615NCTC11022_04895NCTC11126_03635NCTC11181_01361NCTC11341_03646NCTC12650_04327NCTC12950_04423NCTC13216_02715NCTC13846_03877NCTC7922_05814NCTC7927_04506NCTC7928_04614NCTC8009_07321NCTC8179_01378NCTC8450_01118NCTC8500_04545NCTC8621_04201NCTC8622_02683NCTC8959_04844NCTC8960_01561NCTC9001_05431NCTC9007_00458NCTC9036_04023NCTC9044_03185NCTC9050_02025NCTC9055_00966NCTC9062_04215NCTC9073_03393NCTC9111_04264NCTC9117_05052NCTC9119_04266NCTC9434_02611NCTC9701_04377NCTC9702_04759NCTC9703_03434NCTC9706_01336NCTC9777_00471NCTC9969_04264PGD_03811PU06_23035RG28_03905RK56_027990RX35_04903SAMEA3472043_02527SAMEA3472044_04156SAMEA3472047_02499SAMEA3472055_02629SAMEA3472056_00972SAMEA3472070_02394SAMEA3472080_03753SAMEA3472090_04488SAMEA3472108_03200SAMEA3472110_04512SAMEA3472112_04652SAMEA3472114_03619SAMEA3472147_00381SAMEA3484427_01376SAMEA3484429_01105SAMEA3484434_01148SAMEA3485101_01107SAMEA3752372_04459SAMEA3752553_02894SAMEA3752557_00875SAMEA3752559_03711SAMEA3752620_02091SAMEA3753064_03371SAMEA3753097_03906SAMEA3753164_02432SAMEA3753290_00394SAMEA3753300_01862SK85_00169SY51_00970U12A_00179U14A_00178UC41_07425UN86_07710UN91_10575WQ89_09560WR15_02335YDC107_3395

UniProt
Find proteins for C3TPM7 (Escherichia coli)
Explore C3TPM7 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB

Download Ideal Coordinates CCD File 
H [auth C], I [auth C]LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
K [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], J [auth C], L [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.51α = 90
b = 109.77β = 90
c = 195.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-04-14 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Thirup, S.S.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references