4N9I

Crystal Structure of Transcription regulation protein CRP complexed with cGMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers.

Seok, S.H.Im, H.Won, H.S.Seo, M.D.Lee, Y.S.Yoon, H.J.Cha, M.J.Park, J.Y.Lee, B.J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1726-1742

  • DOI: 10.1107/S139900471400724X
  • Primary Citation of Related Structures:  
    4N9H, 4N9I

  • PubMed Abstract: 
  • The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors ...

    The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in a syn conformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.


    Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catabolite gene activatorA, B, C, D210Escherichia coliMutation(s): 0 
Gene Names: 
crpBN17_32921ECs4208LF82_0356A6581_05085A6V01_03575A8C65_03440A9819_19140A9P13_02140A9R57_01495A9X72_01965AAW05_02165AC067_12020AC789_1c37260ACN002_3437ACN68_15060ACN81_28305ACU57_16420ACU90_16115AJ318_13085AM270_08275AM446_03515AM464_09440AM465_06750AMK83_08080AML07_01485AML35_23735APT94_00690APU18_01780APZ14_13205ARC77_13165AU473_04975AUQ13_09460AUS26_07705AW059_21615AW106_07060AWB10_02050AWE53_006700AWF59_010860AWG78_014895AWG90_021360AWP75_19140AZZ83_001627B6V57_18920B7C53_02955B9M99_04965B9N33_12085B9T59_15415BANRA_01989BANRA_03627BANRA_04145BANRA_04354BB545_12035BE963_07620BEN53_20540BER14_21670BFD68_11175BHF03_09490BHF46_11025BHJ80_22735BHS81_20115BHS87_18845BIQ87_18890BIZ41_05790BJJ90_01910BK248_06130BK292_07860BK296_10615BK334_22755BK373_20590BK375_09025BK383_21300BMA87_10595BMT49_24775BMT91_03425BOH76_07185BON63_01455BON65_25075BON66_27530BON69_10200BON71_12975BON72_01385BON75_20170BON76_01810BON83_22260BON86_09485BON87_12775BON91_10370BON92_08215BON94_27575BON95_18995BON96_09110BON98_09540BTQ04_09395BTQ06_10840BvCms12BK_05092BvCms2454_03737BvCms28BK_00204BvCms35BK_03590BvCmsC61A_04704BvCmsHHP001_02893BvCmsHHP019_05289BvCmsHHP056_00460BvCmsKKP036_03607BvCmsKKP061_02735BvCmsKSNP073_02767BvCmsKSNP081_00793BvCmsKSNP120_01760BvCmsKSP011_02542BvCmsKSP024_02693BvCmsKSP026_04148BvCmsKSP045_00177BvCmsKSP058_03245BvCmsKSP067_01765BvCmsKSP076_02835BvCmsNSNP036_05041BvCmsNSP006_03085BvCmsNSP007_00555BvCmsNSP047_05146BvCmsNSP072_04781BvCmsOUP014_04410BvCmsSINP011_03167BvCmsSINP022_03099BvCmsSIP019_00640BvCmsSIP044_03020BW690_18025BWI89_21205BWP17_00110BXT93_05030BZL31_04535BZL69_05875C2M16_11070C2U48_16670C4K41_12150C4M78_15040C5715_11440C5F72_02295C5P01_16600C5P44_10340C6669_11215C6B13_14045C7B02_12645C7B06_17330C7B07_17945C7B08_15185C7B18_18115C9098_10540C9114_07880C9141_09945C9160_13365C9162_17330C9201_10030C9306_01065C9E25_11865C9E67_02575C9Z03_22215C9Z23_06590C9Z28_04325C9Z29_10115C9Z37_07295C9Z39_11650C9Z43_11125C9Z68_19280C9Z69_06430C9Z70_12505C9Z78_23580C9Z89_04880CCZ14_23510CCZ17_12130CDC27_17895CDL37_27995CF006_07935CG692_18420CI641_010070CI693_24745CI694_15790CJU63_19945CJU64_19835CMR93_04485CO706_15435COD30_09250COD46_15600CQB02_21590CQP61_02885CR538_02195CR539_22050CRD98_08275CRE06_04285CRJUMX01_310052CRM83_22695CRT43_20215CRX46_13135CSB64_14655CT146_14655CUB99_15245CV83915_02753CVH05_26630CWM24_10450CWS33_10910D2184_12050D2185_11265D2188_05220D3821_03395D3822_14270D3M98_13045D3O91_13000D3P01_15680D3P02_22735D3Y67_21000D4011_03920D4023_14050D4074_03885D4628_07685D4636_07485D4638_05375D4660_04280D4718_04895D4L91_03870D4M06_04790D4M76_18210D4U49_05005D4U85_06340D4V08_06650D5H35_05070D5I97_02770D6004_04780D6C36_04985D6D43_03500D6T60_05930D6T98_05015D6W00_16140D6X36_10795D6X63_01870D6X76_03180D7K33_03145D7K63_10765D7K66_03345D7W70_11000D7Y10_09355D7Z75_08465D8Y65_23020D9610_03560D9C99_10445D9D20_14185D9D31_04495D9D33_11895D9D43_04095D9D44_15250D9D94_11655D9E13_12730D9E19_06755D9E34_05450D9E35_12130D9E49_05440D9E73_11730D9F17_11915D9F32_08990D9F87_15865D9G11_02100D9G29_06430D9G42_17380D9G48_02405D9G69_07530D9G95_11790D9H10_11370D9H36_04605D9H53_09220D9H68_04090D9H70_15960D9H94_02440D9I18_06290D9I20_11115D9I37_09250D9I87_01380D9I88_04445D9I97_06255D9J03_02880D9J11_12745D9J44_13140D9J46_20450D9J52_09680D9J58_09430D9J60_16375D9J63_07590D9J78_14950D9K02_13795D9K54_11610D9L89_04245D9L99_08255D9S45_19980D9X77_03720D9X97_04695D9Z28_01165DAH18_12510DAH26_09715DAH30_05150DAH32_04190DAH34_07615DAH37_14990DAH43_07480DB359_16535DD762_11900DEN86_18525DEN89_12355DEN97_19485DEO04_11450DEO19_06975DEO20_18420DIV22_04510DJ487_16555DJ492_02060DJ503_12065DK132_14255DL251_09120DL257_10295DL292_01215DL326_09075DL455_03700DL479_03965DL530_02850DL545_02795DL705_01830DL800_24125DL979_12825DLT82_01025DLU50_02285DLU67_09380DLU82_04840DLW60_03945DLW88_06080DLX38_03735DLX40_09940DLY41_03325DLY44_11515DM102_16440DM129_05085DM155_04640DM267_05535DM272_09390DM280_03550DM296_01595DM382_01060DM820_08750DM962_05260DM973_03435DMC44_17055DMI04_03085DMI53_05960DMO02_04590DMY83_06380DMZ50_22180DN627_01880DN660_08540DN700_07425DN703_03545DN808_02825DNB37_04685DNC98_11105DND16_12670DND79_07095DNI21_00110DNJ62_06075DNK12_04295DNQ45_16825DNR35_03795DNR41_15360DNW42_00110DNX19_00110DNX30_18290DOE35_04170DOM23_07420DOS18_03960DOT81_05715DOU81_04015DOY22_03155DOY56_04145DOY61_09690DOY67_04200DP258_06245DP265_00110DP277_13175DQE91_04200DQF36_04440DQF57_08545DQF71_03825DQF72_00110DQG35_05565DQO13_09525DQP61_03245DRP48_06920DRW19_01820DS143_04110DS721_04490DS732_24565DS966_15035DT034_11620DTL43_13855DTL90_06820DTM10_13095DTM45_15670DTZ20_04995DU309_11995DU321_12215DU333_19100DVB38_03910DW236_02765DWB25_02370DXT69_02405DXT71_09280DXT73_15440DXX80_010345E0I42_11555E0K84_11875E0L04_12645E0L12_09595E2112_04305E2114_05490E2115_14900E2119_04475E2127_11680E2128_03050E2129_07770E2134_14615E2135_05900E2148_15245E2855_04304E2863_04750E4K60_09485E4K61_10035E5P22_13775E5P24_08455E5P28_08960E5P37_08510E5S42_07755E5S56_12820E5S58_13660E5S61_12570E5S62_11590EA159_08785EA164_10440EA167_09685EA174_11410EA184_08625EA189_15290EA191_08135EA198_13195EA200_13675EA203_09305EA213_09185EA214_21680EA218_23025EA222_19740EA223_18260EA225_11905EA231_09110EA232_10025EA233_08760EA235_12035EA239_12335EA242_13190EA245_12020EA247_12050EA250_09580EA410_11765EA429_12645EA433_12705EA434_09645EA435_12210EA834_09415EAI42_08950EAI52_04820EAM59_02940EAN70_04855EAN77_07275EAX79_10945EB476_18825EB509_08785EB510_20615EB515_05935EB525_RS14315EBA46_05145EBA84_04735EBJ06_05020EBM08_02780EC1094V2_297EC3234A_57c00190EC382_22180EC95NR1_02737ECONIH1_19655ECTO124_00428ECTO6_00392ED178_04610ED225_03155ED307_08505ED600_01085ED607_00100ED611_03160ED648_05430ED903_02990ED944_06170EEA45_09135EEP23_09625EF082_07140EF173_09685EG075_11775EG599_02890EG796_05605EG808_12455EGC26_08315EGT48_13280EGU87_02890EH186_19910EH412_04985EHD45_03375EHD63_04160EHD79_06120EHJ36_04010EHJ66_05000EHV81_13415EHV90_00965EHW09_01150EHX09_02830EI021_10295EI032_06800EIA08_11980EIA21_13980EIZ93_01465EJ366_25195EJC75_15965EKI52_17450EL75_0338EL79_0357EL80_0349ELT17_21685ELT22_10290ELT23_15700ELT33_18520ELT48_16785ELT49_16685ELT58_15525ELU82_07430ELU85_15745ELU96_12120ELV00_07785ELV05_17245ELV08_20070ELV13_21220ELV15_15520ELV22_20455ELV24_08865ELV28_09785ELX56_05950ELX76_05215ELX79_21675ELX83_07415ELY05_18465ELY23_11815ELY24_17365ELY41_17020ELY48_13545ELY50_07110EO241_03680EPS76_12615EPS91_02550EPS94_12475EPT01_14275EPU41_18890EQ820_13430EQ823_10105EQ825_09745EQ830_06495EQO00_01955ERL57_18400ERS085365_00966ERS085366_00178ERS085374_01444ERS085379_03734ERS085383_01632ERS085386_02309ERS085404_01603ERS085406_01899ERS085411_00374ERS085416_02871ERS139211_00050ERS150873_03047ERS150876_01853EST51_02005EVY14_06885EWK56_16140EXM29_02535ExPECSC019_04608ExPECSC038_01191ExPECSC065_03743EXX06_06165EXX13_13935EXX23_08840EXX53_12615EXX55_04085EXX71_09785EXX78_08635EXX87_01840EYX82_20405EYX99_23150EYY27_22445EYY34_26215EYY78_09450F1E19_05900F7F00_08605F7F11_11960F7F18_08290F7F23_05095F7F26_04885F7F29_09185F7F56_06480F7G01_04690F7G03_06455F9040_03370F9050_05845F9059_08145F9225_09795F9B07_12715F9X20_02245F9Z53_13860F9Z74_11290FAF34_029505FE846_05310FKO60_13850FNJ67_02750FNJ69_15595FNJ83_21300FORC82_0405FPI65_20600FQ021_15115FQ022_15395FQ915_25455FQR64_02305FQU83_03685FQZ46_12775FRV13_19730FV293_08740FV295_03035FV438_16010FVB16_17495FY127_06165FZ043_22770FZC17_21345FZN06_21290FZN26_22660FZN30_07930G3565_08930G3V64_07675G5603_11130G5608_14000G5616_10600G5632_11360G5668_06270G5670_06395G5675_06380G5680_05710G5686_16710G5688_08800G5696_11000G5697_10160GFU40_13930GFU45_13465GFU47_12190GHR40_06765GII67_20365GII91_09775GIJ01_02700GIY13_07245GIY19_10880GJ11_21675GJ638_00885GJD97_02160GKE15_06695GKE16_08210GKE22_04850GKE24_09730GKE26_06700GKE29_04895GKE31_06660GKE39_05430GKE46_03710GKE53_03295GKE58_06205GKE60_06260GKE64_03710GKE69_04600GKE77_07040GKE79_05005GKE87_02415GKE92_07435GKE93_18885GKE98_09105GKF00_16425GKF03_13415GKF21_04865GKF28_04125GKF34_04935GKF39_12070GKF47_04930GKF52_05585GKF74_10180GKF86_11465GKF89_12345GKG08_01315GKG09_01315GKG11_02040GKG12_07255GKG22_02040GKG29_02040GN312_07380GNZ00_11735GNZ02_05105GNZ03_12265GNZ05_15775GP650_08485GP654_12025GP661_06970GP662_20150GP664_09400GP666_13435GP671_08885GP678_11980GP689_12275GP698_14600GP700_18030GP711_17510GP712_06195GP720_16620GP727_14590GP892_17805GP912_17500GP935_13815GP945_09195GP946_11240GP950_10225GP954_11630GQA23_21490GQA63_05605GQA64_04100GQE22_14650GQE30_03550GQE33_13845GQE34_02935GQE36_22280GQE42_03585GQE47_07190GQE51_08365GQE58_14940GQE64_08005GQE68_09775GQE87_03980GQE88_13445GQE93_03265GQF59_06835GQM04_08950GQM06_15625GQM09_05320GQM10_10205GQM13_20765GQM17_11115GQM18_12430GQM28_06385GQN16_12805GQN24_10635GQN33_13955GQS26_16590GQY14_11555GRW12_20745GRW27_10195GRW30_09030GRW42_13985GRW57_17415GRW80_08890GRW81_14100GUB08_08895GUB85_17240GUB91_16235GUB95_19130GUC01_14505GUC12_17260GUC40_09445GUI16_12680GUI33_18150GZS12_01995HmCms169_00412HmCms184_03623HmCmsJML074_03332HmCmsJML079_03341HmCmsJML146_04964HmCmsJML204_01477HmCmsJML236_00132HMPREF3040_00567HW43_21655MJ49_13520MS6198_38620MS8345_03707NCTC10082_02782NCTC10089_00460NCTC10090_03485NCTC10418_00642NCTC10429_01028NCTC10766_02419NCTC10767_01464NCTC10865_00613NCTC10963_00398NCTC10974_00491NCTC11022_03536NCTC11126_02705NCTC11181_02696NCTC11341_01936NCTC12650_00649NCTC12950_00423NCTC13216_01407NCTC13846_00456NCTC7927_00493NCTC7928_02562NCTC8179_05897NCTC8450_04895NCTC8500_00264NCTC8621_00464NCTC8622_00559NCTC8959_03303NCTC8960_03028NCTC9001_04188NCTC9007_04577NCTC9036_00497NCTC9044_01404NCTC9045_00499NCTC9050_03569NCTC9055_02326NCTC9058_01434NCTC9062_02747NCTC9073_00445NCTC9075_00660NCTC9111_00825NCTC9119_00483NCTC9434_00374NCTC9701_00537NCTC9702_00492NCTC9703_04923NCTC9706_02630NCTC9777_01832NCTC9969_00615PGD_00528PU06_13810RG28_21835RK56_021110RX35_03124SAMEA3472043_04072SAMEA3472044_01106SAMEA3472047_01939SAMEA3472055_01380SAMEA3472056_01963SAMEA3472070_03588SAMEA3472080_02881SAMEA3472090_03965SAMEA3472108_04491SAMEA3472110_01311SAMEA3472112_00637SAMEA3472114_02331SAMEA3472147_01069SAMEA3484427_00019SAMEA3484429_02790SAMEA3484434_02659SAMEA3485101_02432SAMEA3752372_00892SAMEA3752553_01011SAMEA3752557_02008SAMEA3752559_00403SAMEA3752620_02651SAMEA3753064_01802SAMEA3753097_01513SAMEA3753164_01987SAMEA3753290_02456SAMEA3753300_02284SK85_03673SY51_19250U12A_03592U14A_03589UC41_08790UN86_22535UN91_22610WQ89_11770WR15_02730YDC107_2012

UniProt
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Go to UniProtKB:  C3SQJ7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCG (Subject of Investigation/LOI)
Query on PCG

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PCG Binding MOAD:  4N9I Kd: 2.56e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.568α = 90
b = 56.171β = 90.18
c = 186.718γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release