7AFI

Bacterial 30S ribosomal subunit assembly complex state C (body domain)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.

Schedlbauer, A.Iturrioz, I.Ochoa-Lizarralde, B.Diercks, T.Lopez-Alonso, J.P.Lavin, J.L.Kaminishi, T.Capuni, R.Dhimole, N.de Astigarraga, E.Gil-Carton, D.Fucini, P.Connell, S.R.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf7547
  • Primary Citation of Related Structures:  
    7AF3, 7AF5, 7AF8, 7AFA, 7AFD, 7AFH, 7AFI, 7AFK, 7AFL, 7AFN, 7AFO, 7AFQ, 7AFR, 7BOD, 7BOE, 7BOF, 7BOG, 7BOH, 7BOI, 7NAR, 7NAS, 7NAT, 7NAU, 7NAV, 7NAX

  • PubMed Abstract: 

    While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo-electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30 S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16 S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.


  • Organizational Affiliation

    Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4B [auth D]206Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5C [auth E]167Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6D [auth F]135Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8E [auth H]130Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11F [auth K]129Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12G [auth L]124Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15H [auth O]89Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16I [auth P]82Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17J [auth Q]84Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18K [auth R]75Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20L [auth T]87Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome maturation factor RimPM [auth X]151Escherichia coliMutation(s): 0 
Gene Names: 
rimPyhbCA6581_13520A6592_14330A6V01_00515A8C65_02275A9819_18200A9P13_03050A9R57_12705A9X72_02945AC067_23780AC789_1c35400ACN002_3263ACU57_14550ACU90_11670AJ318_05135AM270_15615AM446_04425AM464_08475AM465_07740AMK83_06445AML07_19235AML35_13990APT94_23095APU18_16510APZ14_04190ARC77_12300AU473_05840AUQ13_02970AUS26_18365AW059_15280AW106_13165AWB10_02960AWE53_007750AWF59_011795AWG78_015830AWG90_020515AZZ83_001444B6V57_17915B7C53_06465B9M99_10360B9N33_16975B9T59_16360BANRA_01790BANRA_03978BANRA_04186BB545_09885BEN53_19595BFD68_02460BHF03_08615BHF46_07210BHS81_19095BHS87_17860BIQ87_17930BIU72_05300BIZ41_14495BJJ90_02875BK248_21925BK292_10325BK296_12945BK334_09665BK373_10280BK375_17180BK383_15860BMA87_01190BMT49_25700BMT91_09135BvCms12BK_01026BvCms2454_04843BvCms28BK_03353BvCms35BK_01522BvCmsC61A_01482BvCmsHHP019_03132BvCmsHHP056_02505BvCmsKKP036_00265BvCmsKKP061_00867BvCmsKSNP073_02141BvCmsKSNP081_00265BvCmsKSNP120_03551BvCmsKSP011_02071BvCmsKSP024_00304BvCmsKSP026_00481BvCmsKSP045_01629BvCmsKSP058_01861BvCmsKSP067_01443BvCmsKSP076_01609BvCmsNSNP036_02130BvCmsNSP006_04619BvCmsNSP007_02230BvCmsNSP047_04139BvCmsNSP072_03166BvCmsOUP014_03611BvCmsSINP011_04479BvCmsSINP022_03542BvCmsSIP019_00386BvCmsSIP044_00116BWI89_22175C2M16_04320C2U48_17655C4K41_03675C4M78_03215C5715_22690C5N07_18175C5P01_18940C5P44_00535C6669_12125C6B13_18120C7235_03330C7B02_15770C7B06_16695C7B07_10705C7B08_03460C7B18_13725C9098_07895C9114_15350C9141_00495C9160_02445C9162_04215C9201_13770C9306_00520C9E25_11375C9E67_03480C9Z03_07385C9Z23_02310C9Z28_00490C9Z29_07085C9Z37_14765C9Z39_14380C9Z43_00485C9Z69_11070C9Z70_06870C9Z78_03420C9Z89_09170CA593_10450CCZ14_12150CCZ17_15250CDC27_16980CDL37_12105CF006_16775CG692_07190CI641_009150CI693_03565CI694_20945CIG45_16155CJU63_19030CJU64_18910CMR93_08945CO706_14525COD30_12805COD46_10650CQB02_14455CQP61_03755CR538_03180CR539_21140CRD98_04820CRE06_06720CRJUMX01_260087CRM83_23605CRT43_19210CRX46_03850CSB64_06490CT146_02950CUB99_16240CVH05_10885CWM24_22975CWS33_08270D0X26_08985D1912_12210D2184_10400D2185_00550D2188_02685D3821_08430D3822_14680D3M98_06670D3O91_07730D3P01_09055D3P02_05570D3Y67_18395D4011_13620D4074_02330D4628_02550D4636_02785D4638_00685D4660_02725D4718_08975D4L91_11845D4M06_11120D4U49_10465D4U85_14225D4V08_01260D5H35_09675D5I97_10565D6004_08020D6C36_14055D6D43_15405D6T60_15285D6T98_02305D6W00_13910D6X36_05255D6X63_01325D6X76_04230D7K33_12750D7K63_12115D7K66_04390D7W70_15750D7Y10_03485D7Z75_02840D8Y65_13370D9610_07705D9C99_05015D9D31_09850D9D33_00515D9D43_03510D9D44_04305D9D94_03385D9E13_09760D9E19_10295D9E34_10730D9E49_09490D9E73_12375D9F17_07095D9F32_01135D9G11_02975D9G29_06920D9G42_16795D9G48_22395D9G69_00995D9G95_16980D9H10_06565D9H36_12500D9H53_01090D9H68_07455D9H70_01525D9H94_03415D9I18_07070D9I20_02730D9I37_14605D9I87_04955D9I88_16545D9I97_11395D9J11_01025D9J44_07745D9J46_20545D9J52_07810D9J58_06005D9J60_11080D9J63_16805D9J78_05025D9K02_05975D9K48_12150D9K54_17935D9L89_05265D9L99_02555D9S45_00150D9X77_02225D9X97_03015D9Z28_03265DAH18_20505DAH26_17210DAH30_12980DAH32_14080DAH34_01875DAH37_04360DAH43_16675DB359_10675DBQ99_04145DD762_19135DEN86_08165DEN89_09300DEN97_16030DEO04_19500DEO19_06325DEO20_07555DIV22_03080DJ487_12870DJ492_21815DJ503_10870DK132_15395DL251_15040DL257_05545DL292_14605DL326_05955DL455_12595DL479_06485DL530_21135DL545_03765DL705_01195DL800_23160DL979_03350DLT82_02550DLU50_08445DLU67_08270DLU82_10225DLW60_07385DLW88_04690DLX38_07775DLY41_08050DLY44_02205DM102_15060DM129_03900DM155_07540DM267_13960DM272_02325DM280_08950DM296_04730DM382_07255DM820_04520DM962_02535DM973_04545DMC44_07025DMI04_04165DMI53_12610DMO02_15300DMY83_09815DMZ50_12315DN660_01225DN700_04490DN703_00975DN808_01785DNB37_13600DNC98_07055DND16_06430DND79_01225DNI21_14825DNJ62_11965DNK12_02730DNQ45_19755DNR35_05290DNR41_11080DNW42_05300DNX19_05475DNX30_11260DOE35_12505DOM23_01535DOS18_12925DOT81_04150DOU81_12270DOY22_13980DOY56_12140DOY61_04590DOY67_01180DP265_06450DP277_10000DQE91_01160DQF36_20850DQF57_03510DQF71_07055DQF72_06355DQG35_02725DQO13_01190DQP61_01665DRP48_13805DRW19_01190DS143_06665DS721_10985DS732_23590DS966_19175DT034_01165DTL43_04190DTM10_07090DTM45_14405DTZ20_11985DU309_11240DU321_08565DU333_16815DVB38_07290DW236_11980DWB25_03315DXT69_05625DXT71_00545DXT73_13265DXX80_009485E0I42_14235E0K84_20585E0L04_19770E0L12_03810E2112_05640E2114_08285E2115_05735E2119_05765E2127_02470E2128_02600E2129_05655E2134_15700E2135_07975E2148_12390E2855_04121E2863_03946E4K55_06555E4K60_03320E4K61_09175E5P22_12890E5P28_13015E5P37_13240E5S42_11910E5S46_04245E5S47_02865E5S56_15530E5S58_02830E5S61_05810EA159_13410EA167_07035EA189_10710EA191_13025EA198_19520EA200_07260EA203_14945EA213_02390EA214_08705EA218_15110EA222_06430EA225_06975EA231_14825EA232_14625EA233_06070EA242_07640EA245_09665EA250_06530EA410_15875EA429_03180EA434_19670EA435_15260EA834_14920EAI42_15040EAI46_15085EAI52_09995EAM59_00915EAN70_10640EAN77_10380EAX79_13125EB476_09145EB509_07095EB510_12300EB515_06920EBA46_01560EBA84_05725EBJ06_06030EBM08_05350EC3234A_53c00490EC3426_04319EC382_14550EC95NR1_02552ECONIH1_18750ECTO124_00619ECTO6_00586ED225_04165ED307_11680ED600_09295ED607_10320ED611_04175ED648_02810ED903_04550ED944_07155EEA45_06835EEP23_06195EF082_03885EF173_16900EG075_10005EG599_06060EG796_01085EG808_04740EGC26_04810EGT48_12345EGU87_04110EH186_10365EH412_00890EHD45_09310EHD63_05170EHD79_19375EHH55_24255EHJ36_00890EHJ66_05985EHV81_00450EHV90_06065EHW09_05495EHX09_11690EI021_03960EI028_15155EI032_08700EI041_02105EIA08_12605EIA21_02775EIZ93_15760EJ366_26100EJC75_15120EKI52_18340ELT17_03400ELT20_05150ELT22_04740ELT23_06870ELT33_08790ELT48_07015ELT49_04545ELT58_00540ELU82_09410ELU85_07030ELU96_15070ELV05_02170ELV08_03090ELV13_06450ELV15_01725ELV22_10740ELV24_06460ELV28_06240ELX56_11845ELX70_11310ELX76_04020ELX79_02845ELX83_01980ELY05_03155ELY23_12930ELY24_06190ELY41_02060ELY48_01080ELY50_10975EO241_09475EPS76_01470EPS91_00535EPS94_08350EPT01_00520EPU41_18025EQ823_04945EQ825_16430EQ830_04625ERL57_13330ERS085365_00561ERS085366_00575ERS085374_01907ERS085379_00394ERS085383_00718ERS085386_00509ERS085404_02208ERS085406_02910ERS085416_00333ERS139211_00574ERS150873_04325ERS150876_01006EST51_02850EVY14_07620EWK56_02880EXM29_19890ExPECSC019_00733ExPECSC038_02681ExPECSC065_00152EXX06_09585EXX13_07220EXX23_07435EXX24_06255EXX53_05215EXX55_08940EXX71_13295EXX78_16835EXX87_04485EYD11_02750EYX82_02350EYX99_26670EYY27_17450EYY34_08680EYY78_15515F1E13_04755F1E19_22160F7F00_12275F7F11_09140F7F18_01100F7F23_11550F7F26_00510F7F29_05220F7G01_14085F7G03_16255F9059_01215F9Z74_11735FAF34_018990FE846_13840FKO60_06135FNJ67_03680FNJ69_14760FNJ83_20460FQ022_08085FQ915_16575FQR64_03140FQU83_04615FQZ46_16235FRV13_20650FV293_08480FV295_10420FV438_11005FVB16_12900FWK02_30950FY127_14860FZ043_21930GFU40_08290GFU45_16445GFU47_23645GHR40_07700GII67_12855GII91_02620GIY13_09410GIY19_08440GJ11_20705GJ638_05280GJD97_02990GKE15_04560GKE22_12100GKE24_04550GKE26_04235GKE29_02570GKE31_04515GKE39_10640GKE46_11105GKE58_04470GKE60_04205GKE64_10430GKE77_04900GKE87_00805GKE92_01045GKE93_06080GKF00_04240GKF03_05185GKF28_11940GKF34_04535GKF47_04530GKF74_09325GKF86_04155GKF89_14480GKG08_09990GKG09_10130GKG11_10335GKG12_08430GKG22_10250GKG29_10290GN312_06535GNZ00_04975GNZ02_01185GNZ03_06215GP654_17605GP661_13150GP664_11975GP666_12855GP689_13980GP700_08285GP712_11280GP720_14900GP727_07890GP912_13015GP935_13235GP946_08565GP950_18120GQA06_13100GQE22_11445GQE30_02675GQE34_11815GQE42_06055GQE47_10010GQE51_04775GQE58_09360GQE64_09830GQE68_06305GQE88_18540GQE93_14745GQL64_21185GQM06_01810GQM09_10960GQM13_09315GQM17_12990GQN16_09395GQN33_10425GQS26_10800GRW42_15825GRW80_12150HmCms169_01197HmCms184_00230HmCmsJML074_04857HmCmsJML079_04423HmCmsJML146_01154HmCmsJML204_02229HmCmsJML236_03431HW43_20810MJ49_14450MS6198_36560MS8345_03519NCTC10082_02969NCTC10089_00628NCTC10090_03661NCTC10764_04007NCTC10766_02930NCTC10767_01659NCTC10865_00812NCTC10963_00588NCTC11022_03335NCTC11181_02870NCTC12650_00863NCTC13216_01221NCTC13846_00637NCTC7927_00693NCTC7928_02343NCTC8009_01696NCTC8179_06096NCTC8621_00648NCTC8959_03135NCTC8960_03211NCTC9001_05629NCTC9007_04393NCTC9036_00679NCTC9044_01214NCTC9045_00716NCTC9050_03744NCTC9055_02513NCTC9058_01245NCTC9062_02553NCTC9111_00997NCTC9119_00654NCTC9434_00565NCTC9701_00708NCTC9703_05099NCTC9706_02867NCTC9777_02133NCTC9969_00790PGD_03946PU06_19955RG28_20970RK56_014715RX35_04257SAMEA3472043_01802SAMEA3472044_03331SAMEA3472047_01873SAMEA3472055_00399SAMEA3472056_03073SAMEA3472070_01171SAMEA3472080_00946SAMEA3472090_00549SAMEA3472108_00101SAMEA3472110_01542SAMEA3472112_01526SAMEA3472114_00482SAMEA3472147_01879SAMEA3484427_00607SAMEA3484429_00735SAMEA3484434_03594SAMEA3485101_01711SAMEA3752372_01780SAMEA3752553_01186SAMEA3752557_01874SAMEA3752559_03272SAMEA3752620_02342SAMEA3753064_02937SAMEA3753097_03303SAMEA3753164_02301SAMEA3753290_00147SAMEA3753300_02130SK85_03483SY51_18280U12A_03406U14A_03403UC41_24430UN86_15485UN91_15510WQ89_06745WR15_24545YDC107_1843

UniProt
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8A8
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Entity ID: 1
MoleculeChains LengthOrganismImage
16SrRNA1,541Escherichia coli
Sequence Annotations
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
BA [auth A]
BB [auth A]
CA [auth A]
AA [auth A],
AB [auth A],
BA [auth A],
BB [auth A],
CA [auth A],
CB [auth A],
DA [auth A],
DB [auth A],
EA [auth A],
EB [auth A],
FA [auth A],
FB [auth A],
GA [auth A],
GB [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
P [auth A],
PA [auth A],
Q [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
TA [auth A],
U [auth A],
UA [auth A],
V [auth A],
VA [auth A],
W [auth A],
WA [auth A],
X [auth A],
XA [auth A],
Y [auth A],
YA [auth A],
Z [auth A],
ZA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
G [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.9
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainCTQ2017-82222-R
European CommissionSpainPCIG14-GA-2013-632072

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2024-04-24
    Changes: Data collection, Derived calculations, Refinement description