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- EMDB-54790: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subun... -

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Basic information

Entry
Database: EMDB / ID: EMD-54790
TitleCryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)
Map data
Sample
  • Complex: 40S SSU Arabidopsis (root) ribosome complex
    • RNA: x 1 types
    • Protein or peptide: x 12 types
  • Ligand: x 3 types
KeywordsRibosomal 40S subunit -Head region / RIBOSOME
Function / homology
Function and homology information


plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation ...plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / translational initiation / peroxisome / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. ...Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S14/S29 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS13z/uS13y/uS13x / Small ribosomal subunit protein eS28x / Small ribosomal subunit protein uS10z/uS10x / Small ribosomal subunit protein uS14z/uS14y/uS14x / Small ribosomal subunit protein eS19x / Small ribosomal subunit protein uS19x / Small ribosomal subunit protein eS10x / Small ribosomal subunit protein eS17w / Small ribosomal subunit protein eS25y / Small ribosomal subunit protein uS3z ...Small ribosomal subunit protein uS13z/uS13y/uS13x / Small ribosomal subunit protein eS28x / Small ribosomal subunit protein uS10z/uS10x / Small ribosomal subunit protein uS14z/uS14y/uS14x / Small ribosomal subunit protein eS19x / Small ribosomal subunit protein uS19x / Small ribosomal subunit protein eS10x / Small ribosomal subunit protein eS17w / Small ribosomal subunit protein eS25y / Small ribosomal subunit protein uS3z / Small ribosomal subunit protein uS9z / Small ribosomal subunit protein uS7z
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSudeep K / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ ...Sudeep K / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ / Huiskonen JT / Kajander T / Helariutta Y / Paavilainen VO
Funding support United States, Finland, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 Finland
Academy of Finland314672 Finland
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)
Authors: Sudeep K / Paavilainen VO
History
DepositionAug 14, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54790.png

Downloads & links

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Map

FileDownload / File: emd_54790.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.1441967 - 0.3934427
Average (Standard dev.)0.0030326883 (±0.015101179)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54790_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54790_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 40S SSU Arabidopsis (root) ribosome complex

EntireName: 40S SSU Arabidopsis (root) ribosome complex
Components
  • Complex: 40S SSU Arabidopsis (root) ribosome complex
    • RNA: RNA (500-MER)
    • Protein or peptide: Small ribosomal subunit protein uS3z
    • Protein or peptide: Small ribosomal subunit protein uS7z
    • Protein or peptide: Small ribosomal subunit protein uS19x
    • Protein or peptide: Small ribosomal subunit protein uS9z
    • Protein or peptide: Small ribosomal subunit protein uS13z/uS13y/uS13x
    • Protein or peptide: Small ribosomal subunit protein eS19x
    • Protein or peptide: Small ribosomal subunit protein uS10z/uS10x
    • Protein or peptide: Small ribosomal subunit protein eS28x
    • Protein or peptide: Small ribosomal subunit protein uS14z/uS14y/uS14x
    • Protein or peptide: Small ribosomal subunit protein eS25y
    • Protein or peptide: Small ribosomal subunit protein eS10x
    • Protein or peptide: Small ribosomal subunit protein eS17w
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: 40S SSU Arabidopsis (root) ribosome complex

SupramoleculeName: 40S SSU Arabidopsis (root) ribosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: RNA (500-MER)

MacromoleculeName: RNA (500-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 160.514719 KDa
SequenceString: AUUGACGGAA GGGCACCACC AGGAGUGGAG CCUGCGGCUU AAUUUGAC(I2T)C AACACGGGGA AACUUACCAG GU (OMC)CAGACA UAGUAAGGAU UGACAGACUG AGAGCUCUUU CUUGAUUCUA UGGGUGGUG(OMG) UGCAUGGC(4AC)G U UCUUAGUU GGUGGAGCGA ...String:
AUUGACGGAA GGGCACCACC AGGAGUGGAG CCUGCGGCUU AAUUUGAC(I2T)C AACACGGGGA AACUUACCAG GU (OMC)CAGACA UAGUAAGGAU UGACAGACUG AGAGCUCUUU CUUGAUUCUA UGGGUGGUG(OMG) UGCAUGGC(4AC)G U UCUUAGUU GGUGGAGCGA UUUGUCUGGU UAAUUCCGUU AACGAACGAG ACCUCAGCCU GCUAACUAGC UACGUGGAGG CA UCCCUUC ACGGCCGGCU (OMU)CUUAGAGGG ACUAUGGCCG UUUAGGCCAA GGAAGUUUGA GGCAAUAACA (OMG)GUCU GUGA UGCCCUUAGA UGUUCUGGGC CGCACGCGCG CUACACUGAU GUAUUCAACG AGUUCACACC UUGGCCGACA GGCCCG GGU AAUCUUUGAA AUUUCAUCGU GAUGGGGAUA GAUCAUUGCA AUUGUUGGUC UUCAACGAGG AAUUCCUAGU AAGCGCG AG UCAUCAGCUC GCGUUGACUA CGUCCCUGCC CUUUGUACAC ACCG

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Macromolecule #2: Small ribosomal subunit protein uS3z

MacromoleculeName: Small ribosomal subunit protein uS3z / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.559232 KDa
SequenceString: MATQISKKRK FVADGVFYAE LNEVLTRELA EDGYSGVEVR VTPMRTEIII RATRTQNVLG EKGRRIRELT SLVQKRFKFP VDSVELYAE KVNNRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFVMES GAKGCEVIVS GKLRAARAKS MKFKDGYMVS S GQPTKEYI ...String:
MATQISKKRK FVADGVFYAE LNEVLTRELA EDGYSGVEVR VTPMRTEIII RATRTQNVLG EKGRRIRELT SLVQKRFKFP VDSVELYAE KVNNRGLCAI AQAESLRYKL LGGLAVRRAC YGVLRFVMES GAKGCEVIVS GKLRAARAKS MKFKDGYMVS S GQPTKEYI DAAVRHVLLR QGVLGIKVKI MLDWDPTGKS GPKTPLPDVV IIHAPKDDVV YSAPAQAAAP VTLVQEAPLT TV DYPEMIP PVA

UniProtKB: Small ribosomal subunit protein uS3z

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Macromolecule #3: Small ribosomal subunit protein uS7z

MacromoleculeName: Small ribosomal subunit protein uS7z / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.025564 KDa
SequenceString: MAASAEIDAE IQQQLTNEVK LFNRWSFDDV SVTDISLVDY IGVQPSKHAT FVPHTAGRYS VKRFRKAQCP IVERLTNSLM MHGRNNGKK LMAVRIVKHA MEIIHLLSDL NPIQVIIDAI VNSGPREDAT RIGSAGVVRR QAVDISPLRR VNQAIFLLTT G AREAAFRN ...String:
MAASAEIDAE IQQQLTNEVK LFNRWSFDDV SVTDISLVDY IGVQPSKHAT FVPHTAGRYS VKRFRKAQCP IVERLTNSLM MHGRNNGKK LMAVRIVKHA MEIIHLLSDL NPIQVIIDAI VNSGPREDAT RIGSAGVVRR QAVDISPLRR VNQAIFLLTT G AREAAFRN IKTIAECLAD ELINAAKGSS NSYAIKKKDE IERVAKANR

UniProtKB: Small ribosomal subunit protein uS7z

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Macromolecule #4: Small ribosomal subunit protein uS19x

MacromoleculeName: Small ribosomal subunit protein uS19x / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.106266 KDa
SequenceString:
MADVEPEVAA AGVPKKRTFK KFAFKGVDLD ALLDMSTDDL VKLFSSRIRR RFSRGLTRKP MALIKKLRKA KREAPAGEKP EPVRTHLRN MIIVPEMIGS IIGVYNGKTF NQVEIKPEMI GHYLAEFSIS YKPVKHGRPG VGATHSSRFI PLK

UniProtKB: Small ribosomal subunit protein uS19x

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Macromolecule #5: Small ribosomal subunit protein uS9z

MacromoleculeName: Small ribosomal subunit protein uS9z / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.663549 KDa
SequenceString:
MATQPATESV QCFGRKKTAV AVTHCKRGSG LIKLNGCPIE LFQPEILRFK IFEPILLLGK HRFAGVNMRI RVNGGGHTSQ VYAIRQSIA KALVAYYQKY VDEQSKKEIK DILVRYDRTL LVADPRRCEP KKFGGRGARS RYQKSYR

UniProtKB: Small ribosomal subunit protein uS9z

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Macromolecule #6: Small ribosomal subunit protein uS13z/uS13y/uS13x

MacromoleculeName: Small ribosomal subunit protein uS13z/uS13y/uS13x / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.582527 KDa
SequenceString:
MSLVANEEFQ HILRVLNTNV DGKQKIMFAL TSIKGIGRRL ANIVCKKADV DMNKRAGELS AAEIDNLMTI VANPRQFKIP DWFLNRQKD YKDGKYSQVV SNALDMKLRD DLERLKKIRN HRGLRHYWGL RVRGQHTKTT GRRGKTVGVS KKR

UniProtKB: Small ribosomal subunit protein uS13z/uS13y/uS13x

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Macromolecule #7: Small ribosomal subunit protein eS19x

MacromoleculeName: Small ribosomal subunit protein eS19x / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.627091 KDa
SequenceString:
MATGKTVKDV SPHEFVKAYA AHLKRSGKIE LPLWTDIVKT GKLKELAPYD PDWYYIRAAS MARKVYLRGG LGVGAFRRIY GGSKRNGSR PPHFCKSSGG VARHILQQLQ TMNIVDLDTK GGRKITSSGQ RDLDQVAGRI AAA

UniProtKB: Small ribosomal subunit protein eS19x

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Macromolecule #8: Small ribosomal subunit protein uS10z/uS10x

MacromoleculeName: Small ribosomal subunit protein uS10z/uS10x / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.903319 KDa
SequenceString:
MATAYQPMKP GKAGLEEPLE QIHKIRITLS SKNVKNLEKV CTDLVRGAKD KRLRVKGPVR MPTKVLKITT RKAPCGEGTN TWDRFELRV HKRVIDLFSS PDVVKQITSI TIEPGVEVEV TIADS

UniProtKB: Small ribosomal subunit protein uS10z/uS10x

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Macromolecule #9: Small ribosomal subunit protein eS28x

MacromoleculeName: Small ribosomal subunit protein eS28x / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.355558 KDa
SequenceString:
MDSQIKHAVV VKVMGRTGSR GQVTQVRVKF TDSDRFIMRN VKGPVREGDV LTLLESEREA RRLR

UniProtKB: Small ribosomal subunit protein eS28x

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Macromolecule #10: Small ribosomal subunit protein uS14z/uS14y/uS14x

MacromoleculeName: Small ribosomal subunit protein uS14z/uS14y/uS14x / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.443529 KDa
SequenceString:
MGHSNVWNSH PKKYGPGSRL CRVCGNSHGL IRKYGLNCCR QCFRSNAKEI GFIKYR

UniProtKB: Small ribosomal subunit protein uS14z/uS14y/uS14x

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Macromolecule #11: Small ribosomal subunit protein eS25y

MacromoleculeName: Small ribosomal subunit protein eS25y / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.095305 KDa
SequenceString:
MAPKKDKVPP PSSKPAKSGG GKQKKKKWSK GKQKEKVNNM VLFDQGTYDK LLTEAPKFKL ITPSILSDRM RINGSLARRA IRELMAKGL IRMVSAHSSQ QIYTRATNT

UniProtKB: Small ribosomal subunit protein eS25y

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Macromolecule #12: Small ribosomal subunit protein eS10x

MacromoleculeName: Small ribosomal subunit protein eS10x / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.581156 KDa
SequenceString:
MIISEANRKE ICKYLFKEGV CFAKKDFNLA KHPLIDVPNL QVIKLMQSFK SKEYVRETFA WMHYYWFLTN EGIEFLRTYL NLPSDVVPA TLKKSAKPGG RPFGGPPGDR SRGPRHEGGD RPRFGDRDGY RAGPRAGGEF GGEKGGAPAD YQPSFQGSGR G FGRGAGGY SAAAPSGSGL P

UniProtKB: Small ribosomal subunit protein eS10x

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Macromolecule #13: Small ribosomal subunit protein eS17w

MacromoleculeName: Small ribosomal subunit protein eS17w / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.048728 KDa
SequenceString:
MGRVRTKTVK KSSRQVIEKY YSRMTLDFHT NKKILEEVAI IPSKRLRNKI AGFSTHLMKR IQKGPVRGIS LKLQEEERER RMDFVPDES AIKTDEIKVD KETLEMLASL GMSDTPGISA VEPQQAMAPI AAFGGGRAPR RY

UniProtKB: Small ribosomal subunit protein eS17w

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Macromolecule #14: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 14 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / 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 statetissue

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Sample preparation

BufferpH: 7.4
Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor
GridModel: Quantifoil / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 24.512 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 10500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115070
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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