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- EMDB-30296: Cryo-EM structure of yeast Ribonuclease MRP -

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Basic information

Entry
Database: EMDB / ID: EMD-30296
TitleCryo-EM structure of yeast Ribonuclease MRP
Map data
Sample
  • Complex: Ribonuclease MRP
    • RNA: x 1 types
    • Protein or peptide: x 10 types
  • Ligand: x 2 types
KeywordsRibonuclease MRP / RNA-protein complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity ...ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / mRNA processing / rRNA processing / nucleolus / RNA binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Ribonuclease MRP protein subunit RMP1 / RNase P, subunit Pop3 / RNase P subunit Pop3 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal ...: / : / Ribonuclease MRP protein subunit RMP1 / RNase P, subunit Pop3 / RNase P subunit Pop3 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / : / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / POP1 C-terminal domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like
Similarity search - Domain/homology
Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP8 / Ribonucleases P/MRP protein subunit POP7 / RNases MRP/P 32.9 kDa subunit / Ribonuclease P/MRP protein subunit RPP1 / Ribonuclease MRP protein subunit SNM1 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonucleases P/MRP protein subunit POP3 / Ribonuclease MRP protein subunit RMP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLan P / Wu J
CitationJournal: Science / Year: 2020
Title: Structural insight into precursor ribosomal RNA processing by ribonuclease MRP.
Authors: Pengfei Lan / Bin Zhou / Ming Tan / Shaobai Li / Mi Cao / Jian Wu / Ming Lei /
Abstract: Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to ...Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to RNase P, which selectively cleaves transfer RNA-like substrates, it has remained a mystery how RNase MRP recognizes its diverse substrates. To address this question, we determined cryo-electron microscopy structures of RNase MRP alone and in complex with a fragment of pre-rRNA. These structures and the results of biochemical studies reveal that coevolution of both protein and RNA subunits has transformed RNase MRP into a distinct ribonuclease that processes single-stranded RNAs by recognizing a short, loosely defined consensus sequence. This broad substrate specificity suggests that RNase MRP may have myriad yet unrecognized substrates that could play important roles in various cellular contexts.
History
DepositionMay 24, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c79
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30296.png

Downloads & links

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Map

FileDownload / File: emd_30296.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.01
Minimum - Maximum-0.042190913 - 0.10492378
Average (Standard dev.)0.000004687124 (±0.0016471439)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0420.1050.000

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Supplemental data

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Sample components

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Entire : Ribonuclease MRP

EntireName: Ribonuclease MRP
Components
  • Complex: Ribonuclease MRP
    • RNA: Ribonuclease MRP RNA subunit NME1
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP1
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP3
    • Protein or peptide: RNases MRP/P 32.9 kDa subunit
    • Protein or peptide: Ribonuclease P/MRP protein subunit POP5
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP6
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP7
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP8
    • Protein or peptide: Ribonuclease P/MRP protein subunit RPP1
    • Protein or peptide: Ribonuclease MRP protein subunit SNM1
    • Protein or peptide: Ribonuclease MRP protein subunit RMP1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Ribonuclease MRP

SupramoleculeName: Ribonuclease MRP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: s288c

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Macromolecule #1: Ribonuclease MRP RNA subunit NME1

MacromoleculeName: Ribonuclease MRP RNA subunit NME1 / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 108.806703 KDa
SequenceString: AAUCCAUGAC CAAAGAAUCG UCACAAAUCG AAGCUUACAA AAUGGAGUAA AAUUUUGUUU ACUCAGUAAU AUGCUUUGGG UUGAAAGUC UCCCACCAAU UCGUAUGCGG AAAACGUAAU GAGAUUUAAA AAUUUUAAAU UGUUUAAAUC AACUCAUUAA G GAGGAUGC ...String:
AAUCCAUGAC CAAAGAAUCG UCACAAAUCG AAGCUUACAA AAUGGAGUAA AAUUUUGUUU ACUCAGUAAU AUGCUUUGGG UUGAAAGUC UCCCACCAAU UCGUAUGCGG AAAACGUAAU GAGAUUUAAA AAUUUUAAAU UGUUUAAAUC AACUCAUUAA G GAGGAUGC CCUUGGGUAU UCUGCUUCUU GACCUGGUAC CUCUAUUGCA GGGUACUGGU GUUUUCUUCG GUACUGGAUU CC GUUUGUA UGGAAUCUAA ACCAUAGUUA UGACGAUUGC UCUUUCCCGU GCUGGAUCGA GUAACCCAAU GGAGCUUACU AUU CUUGGU CCAUGGAUUC ACCC

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Macromolecule #2: Ribonucleases P/MRP protein subunit POP1

MacromoleculeName: Ribonucleases P/MRP protein subunit POP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.559555 KDa
SequenceString: MSGSLSRGNG GKKVLNKNQL LKRNRIRNAR SIRAEAVAAS STKTGTPSDL SESGSKLNVD QFISSRQFEV KQLQLAMHNS KAASSTRIF QALPRKLRRR TASHNVRRIP KRMRNRALRE MRKSDQQDVL KGSSASSRKA HGLNAKQLYK ARMSIKLLRL A SKSTSMKL ...String:
MSGSLSRGNG GKKVLNKNQL LKRNRIRNAR SIRAEAVAAS STKTGTPSDL SESGSKLNVD QFISSRQFEV KQLQLAMHNS KAASSTRIF QALPRKLRRR TASHNVRRIP KRMRNRALRE MRKSDQQDVL KGSSASSRKA HGLNAKQLYK ARMSIKLLRL A SKSTSMKL SMPPEVTSSN CHVRQKIKTL KRMIKESSTA NPNIKLLNNR MGSYDCTGVN ELAPIPKGRV KYTKRQKHFA WL PTHIWNA KRSHMMKRWG YQMVWAPTQK CFKLTHRLGG DTCSSDGALC MDSSYIGTII VKDKSNDSEG DFLKSIIGKL TAE RANLRK YREGQVLFQG LIYSFNEENG EDSTKPLGPC DVFWVQKDTA IIRLHPSIYT QVFNILLQHK EKLTVQDCRY SLAS VTLKG AKALESLASC LRSTEYSKSF EQFKMVSMIT DHNALPQRCT FAFEAIDPRH LAAPKKLNDS QRKTVNSDDI LSLHE NYPQ DEINAVFNEL CDPESRTQSY NNQNTLKEIS ARRYKLLTAT PNSINKTTVP FKESDDPSIP LVIIRRLKTR DWIVVL PWF WLLPLWHLLN RIPRMYHIGL RQFQQIQYEN KQLYFPDDYP FTQLGYIENS FYKKEASKTK WDRKPMGKRI NFEKIKD IH NTKLPAYSGE IGDFFSSDWR FLQILRNGID YLQRNDKTLE LMDSKKTGQF NAQGVRDINC VNDVLEFCKD YEAKTKAM S LSIEENIPVA LCKNRKCQFR TPDSISVNSS SFSLTFFPRC IIAVSCTLLE RGHPKDNARI YQVPEKDLEH WLQLAKGVY RPNGRKDHDL KIPLPEVHDL IGFITSGTYH LNCGNGMGIG FIDHHAAIRQ PTRYVLIRNV GTNTYRLGEW SKISV

UniProtKB: Ribonucleases P/MRP protein subunit POP1

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Macromolecule #3: Ribonucleases P/MRP protein subunit POP3

MacromoleculeName: Ribonucleases P/MRP protein subunit POP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.643721 KDa
SequenceString: MSGSLKSLDK KIAKRRQVYK PVLDNPFTNE AHMWPRVHDQ PLIWQLLQSS IINKLIHIQS KENYPWELYT DFNEIVQYLS GAHGNSDPV CLFVCNKDPD VPLVLLQQIP LLCYMAPMTV KLVQLPKSAM DTFKSVSKYG MLLLRCDDRV DKKFVSQIQK N VDLLQFPW ...String:
MSGSLKSLDK KIAKRRQVYK PVLDNPFTNE AHMWPRVHDQ PLIWQLLQSS IINKLIHIQS KENYPWELYT DFNEIVQYLS GAHGNSDPV CLFVCNKDPD VPLVLLQQIP LLCYMAPMTV KLVQLPKSAM DTFKSVSKYG MLLLRCDDRV DKKFVSQIQK N VDLLQFPW LNAIKYRPTS VKLLKTTVPI VSKKRQK

UniProtKB: Ribonucleases P/MRP protein subunit POP3

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Macromolecule #4: RNases MRP/P 32.9 kDa subunit

MacromoleculeName: RNases MRP/P 32.9 kDa subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.933168 KDa
SequenceString: MDRTQTFIKD CLFTKCLEDP EKPFNENRFQ DTLLLLPTDG GLTSRLQRQQ RKSKLNLDNL QKVSQLESAD KQLEKRDYQR INKNSKIAL REYINNCKKN TKKCLKLAYE NKITDKEDLL HYIEEKHPTI YESLPQYVDF VPMYKELWIN YIKELLNITK N LKTFNGSL ...String:
MDRTQTFIKD CLFTKCLEDP EKPFNENRFQ DTLLLLPTDG GLTSRLQRQQ RKSKLNLDNL QKVSQLESAD KQLEKRDYQR INKNSKIAL REYINNCKKN TKKCLKLAYE NKITDKEDLL HYIEEKHPTI YESLPQYVDF VPMYKELWIN YIKELLNITK N LKTFNGSL ALLKLSMADY NGALLRVTKS KNKTLIGLQG IVIWDSQKFF IMIVKGNIID EIKCIPKKGT VFQFEIPISD DD DSALRYS ILGDRFKYRS VDRAGRKFKS RRCDDMLYYI QN

UniProtKB: RNases MRP/P 32.9 kDa subunit

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Macromolecule #5: Ribonuclease P/MRP protein subunit POP5

MacromoleculeName: Ribonuclease P/MRP protein subunit POP5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.60159 KDa
SequenceString:
MVRLKSRYIL FEIIFPPTDT NVEESVSKAD ILLSHHRASP ADVSIKSILQ EIRRSLSLNL GDYGSAKCNS LLQLKYFSNK TSTGIIRCH REDCDLVIMA LMLMSKIGDV DGLIVNPVKV SGTIKKIEQF AMRRNSKILN IIKCSQSSHL SDNDFIINDF K KIGRENEN ENEDD

UniProtKB: Ribonuclease P/MRP protein subunit POP5

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Macromolecule #6: Ribonucleases P/MRP protein subunit POP6

MacromoleculeName: Ribonucleases P/MRP protein subunit POP6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.234959 KDa
SequenceString:
MINGVYYNEI SRDLDISSST QCLRFLKETV IPSLANNGNN STSIQYHGIS KNDNIKKSVN KLDKQINMAD RSLGLQQVVC IFSYGPHIQ KMLSILEIFK KGYIKNNKKI YQWNKLTSFD IKREGRNELQ EERLKVPILV TLVSDSEIID LNLHSFTKQ

UniProtKB: Ribonucleases P/MRP protein subunit POP6

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Macromolecule #7: Ribonucleases P/MRP protein subunit POP7

MacromoleculeName: Ribonucleases P/MRP protein subunit POP7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.844284 KDa
SequenceString:
MALKKNTHNK STKRVTKHPS LKTLTHKQIH TTIFVKSTTP YVSALKRINK FLDSVHKQGS SYVAVLGMGK AVEKTLALGC HFQDQKNKK IEVYTKTIEV LDEVITEGQA DIDMESDVED DDKETQLKKR AVSGVELRIY V

UniProtKB: Ribonucleases P/MRP protein subunit POP7

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Macromolecule #8: Ribonucleases P/MRP protein subunit POP8

MacromoleculeName: Ribonucleases P/MRP protein subunit POP8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.530351 KDa
SequenceString:
MGKKTFREWQ YFKLSITSFD QDVDDAHAID QMTWRQWLNN ALKRSYGIFG EGVEYSFLHV DDKLAYIRVN HADKDTFSSS ISTYISTDE LVGSPLTVSI LQESSSLRLL EVTDDDRLWL KKVMEEEEQD CKCI

UniProtKB: Ribonucleases P/MRP protein subunit POP8

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Macromolecule #9: Ribonuclease P/MRP protein subunit RPP1

MacromoleculeName: Ribonuclease P/MRP protein subunit RPP1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.270262 KDa
SequenceString: MLVDLNVPWP QNSYADKVTS QAVNNLIKTL STLHMLGYTH IAINFTVNHS EKFPNDVKLL NPIDIKRRFG ELMDRTGLKL YSRITLIID DPSKGQSLSK ISQAFDIVAA LPISEKGLTL STTNLDIDLL TFQYGSRLPT FLKHKSICSC VNRGVKLEIV Y GYALRDVQ ...String:
MLVDLNVPWP QNSYADKVTS QAVNNLIKTL STLHMLGYTH IAINFTVNHS EKFPNDVKLL NPIDIKRRFG ELMDRTGLKL YSRITLIID DPSKGQSLSK ISQAFDIVAA LPISEKGLTL STTNLDIDLL TFQYGSRLPT FLKHKSICSC VNRGVKLEIV Y GYALRDVQ ARRQFVSNVR SVIRSSRSRG IVIGSGAMSP LECRNILGVT SLIKNLGLPS DRCSKAMGDL ASLVLLNGRL RN KSHKQTI VTGGGSGNGD DVVNDVQGID DVQTIKVVKR SMDAEQLGHA SKRHKP

UniProtKB: Ribonuclease P/MRP protein subunit RPP1

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Macromolecule #10: Ribonuclease MRP protein subunit SNM1

MacromoleculeName: Ribonuclease MRP protein subunit SNM1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.578955 KDa
SequenceString: MNKDQAEKYQ ERSLRQKYNL LHVLPTLNSR ALSGLYYKNF HNSVKRYQIM LPEQLKSGKF CSHCGCVYVP NFNASLQLTT NTEQGDSDE LGGESMEGPK KCIQVNCLNC EKSKLFEWKS EFVVPTFGQD VSPMINSTSS GKVSYAVKKP QKSKTSTGKE R SKKRKLNS ...String:
MNKDQAEKYQ ERSLRQKYNL LHVLPTLNSR ALSGLYYKNF HNSVKRYQIM LPEQLKSGKF CSHCGCVYVP NFNASLQLTT NTEQGDSDE LGGESMEGPK KCIQVNCLNC EKSKLFEWKS EFVVPTFGQD VSPMINSTSS GKVSYAVKKP QKSKTSTGKE R SKKRKLNS LTNLLSKRNQ EKKMEKKKSS SLSLESFMKS

UniProtKB: Ribonuclease MRP protein subunit SNM1

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Macromolecule #11: Ribonuclease MRP protein subunit RMP1

MacromoleculeName: Ribonuclease MRP protein subunit RMP1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.657668 KDa
SequenceString: MDEMDNVIRS LEQEYRLILL LNHRNKNQHR AASWYGSFNE MKRNCGQIIT LFSSRRLQAK RLKDVEWVKL HRLLQRALFR QLKRWYWQF NGVIALGQFV TLGCTLVTLL ANVRALYMRL WEINETEFIR CGCLIKNLPR TKAKSVVNDV EELGEIIDED I GNNVQENE ...String:
MDEMDNVIRS LEQEYRLILL LNHRNKNQHR AASWYGSFNE MKRNCGQIIT LFSSRRLQAK RLKDVEWVKL HRLLQRALFR QLKRWYWQF NGVIALGQFV TLGCTLVTLL ANVRALYMRL WEINETEFIR CGCLIKNLPR TKAKSVVNDV EELGEIIDED I GNNVQENE LVITSIPKPL TENCKKKKKR KKKNKSAIDG IFG

UniProtKB: Ribonuclease MRP protein subunit RMP1

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1232761
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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