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- EMDB-4337: Cryo-EM structure of a late human pre-40S ribosomal subunit - State C -

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Entry
Database: EMDB / ID: 4337
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State C
Map data
SampleCryo-EM structure of a human pre-40S ribosomal subunit with bound PNO1, NOB1, TSR1, BYST, RIOK2 and LTV1
  • nucleic-acidNucleic acid
  • (40S ribosomal protein ...) x 26
  • Ubiquitin-40S ribosomal protein S27a
  • Receptor of activated protein C kinase 1
  • (RNA-binding protein ...) x 2
  • Pre-rRNA-processing protein TSR1 homolog
  • Bystin
  • Serine/threonine-protein kinase RIO2
  • Protein LTV1 homolog
  • ligand
Function / homology40S ribosomal protein S1/3, eukaryotes / Ribosomal S17 / S25 ribosomal protein / Ribosomal protein S27 / Ribosomal protein S27a / S4 domain / Ribosomal protein S24e / Ribosomal protein S7e / Ribosomal protein S21e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family ...40S ribosomal protein S1/3, eukaryotes / Ribosomal S17 / S25 ribosomal protein / Ribosomal protein S27 / Ribosomal protein S27a / S4 domain / Ribosomal protein S24e / Ribosomal protein S7e / Ribosomal protein S21e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal S3Ae family / Ribosomal family S4e / KOW motif / Low temperature viability protein / Ribosomal protein S15 / Pre-rRNA-processing protein PNO1-like / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S2 / Ribosomal protein S13/S18 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / RNA-binding protein NOB1 / Ribosomal protein S19e signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S4 signature. / Ubiquitin domain signature. / Ribosomal protein S13 signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S17e signature. / Ribosomal protein S7e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S19 signature. / Ribosomal protein S17 signature. / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Putative WW-binding domain and destruction box / Bystin / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / AARP2CN (NUC121) domain / Nin one binding (NOB1) Zn-ribbon like / Rio2, N-terminal / 40S ribosomal protein S4 C-terminus / Ribosomal protein S12 signature. / 40S ribosomal protein SA C-terminus / Ribosomal_S17 N-terminal / PIN domain of ribonuclease / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / NOB1, PIN domain / Ribosome biogenesis protein Bms1/Tsr1 / Ribosomal protein S21e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin / Ubiquitin conserved site / WD40 repeat, conserved site / RIO kinase, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S7, conserved site / Nin one binding (NOB1) Zn-ribbon-like / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / RIO2 kinase winged helix domain, N-terminal / Ribosomal protein S2, conserved site / WD40/YVTN repeat-like-containing domain superfamily / Ribonuclease Nob1, eukaryote
Function and homology information
SourceHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsAmeismeier M / Cheng J / Berninghausen O / Beckmann R
CitationJournal: Nature / Year: 2018
Title: Visualizing late states of human 40S ribosomal subunit maturation.
Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann
Validation ReportPDB-ID: 6g18

SummaryFull reportAbout validation report
DateDeposition: Mar 20, 2018 / Header (metadata) release: May 2, 2018 / Map release: Jun 6, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0683
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0683
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6g18
  • Surface level: 0.0683
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4337.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.08 Å/pix.
= 390.24 Å
360 pix
1.08 Å/pix.
= 390.24 Å
360 pix
1.08 Å/pix.
= 390.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour Level:0.0583 (by author), 0.0683 (movie #1):
Minimum - Maximum-0.21051593 - 0.47002733
Average (Standard dev.)0.0013010966 (0.01320922)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 390.24 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z390.240390.240390.240
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2110.4700.001

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Supplemental data

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Sample components

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Entire Cryo-EM structure of a human pre-40S ribosomal subunit with bound...

EntireName: Cryo-EM structure of a human pre-40S ribosomal subunit with bound PNO1, NOB1, TSR1, BYST, RIOK2 and LTV1
Details: Cytoplasmic precursor of the human small ribosomal subunit (pre-40S) purified by affinity chromatography using the StFLAG-tagged ribosomal biogenesis factor PNO1
Number of components: 37

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Component #1: protein, Cryo-EM structure of a human pre-40S ribosomal subunit w...

ProteinName: Cryo-EM structure of a human pre-40S ribosomal subunit with bound PNO1, NOB1, TSR1, BYST, RIOK2 and LTV1
Details: Cytoplasmic precursor of the human small ribosomal subunit (pre-40S) purified by affinity chromatography using the StFLAG-tagged ribosomal biogenesis factor PNO1
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: nucleic-acid, pre-18S ribosomal RNA

Nucleic-acidName: pre-18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGCUCG CUCCUCUCCU ACUUGGAUAA CUGUGGUAAU UCUAGAGCUA AUACAUGCCG ACGGGCGCUG ACCCCCUUCG CGGGGGGGAU GCGUGCAUUU AUCAGAUCAA AACCAACCCG GUCAGCCCCU CUCCGGCCCC GGCCGGGGGG CGGGCGCCGG CGGCUUUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCCCCGUGG CGGCGACGAC CCAUUCGAAC GUCUGCCCUA UCAACUUUCG AUGGUAGUCG CCGUGCCUAC CAUGGUGACC ACGGGUGACG GGGAAUCAGG GUUCGAUUCC GGAGAGGGAG CCUGAGAAAC GGCUACCACA UCCAAGGAAG GCAGCAGGCG CGCAAAUUAC CCACUCCCGA CCCGGGGAGG UAGUGACGAA AAAUAACAAU ACAGGACUCU UUCGAGGCCC UGUAAUUGGA AUGAGUCCAC UUUAAAUCCU UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGC UGCAGUUAAA AAGCUCGUAG UUGGAUCUUG GGAGCGGGCG GGCGGUCCGC CGCGAGGCGA GCCACCGCCC GUCCCCGCCC CUUGCCUCUC GGCGCCCCCU CGAUGCUCUU AGCUGAGUGU CCCGCGGGGC CCGAAGCGUU UACUUUGAAA AAAUUAGAGU GUUCAAAGCA GGCCCGAGCC GCCUGGAUAC CGCAGCUAGG AAUAAUGGAA UAGGACCGCG GUUCUAUUUU GUUGGUUUUC GGAACUGAGG CCAUGAUUAA GAGGGACGGC CGGGGGCAUU CGUAUUGCGC CGCUAGAGGU GAAAUUCUUG GACCGGCGCA AGACGGACCA GAGCGAAAGC AUUUGCCAAG AAUGUUUUCA UUAAUCAAGA ACGAAAGUCG GAGGUUCGAA GACGAUCAGA UACCGUCGUA GUUCCGACCA UAAACGAUGC CGACCGGCGA UGCGGCGGCG UUAUUCCCAU GACCCGCCGG GCAGCUUCCG GGAAACCAAA GUCUUUGGGU UCCGGGGGGA GUAUGGUUGC AAAGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGAAA CCUCACCCGG CCCGGACACG GACAGGAUUG ACAGAUUGAU AGCUCUUUCU CGAUUCCGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCUGGUUAA UUCCGAUAAC GAACGAGACU CUGGCAUGCU AACUAGUUAC GCGACCCCCG AGCGGUCGGC GUCCCCCAAC UUCUUAGAGG GACAAGUGGC GUUCAGCCAC CCGAGAUUGA GCAAUAACAG GUCUGUGAUG CCCUUAGAUG UCCGGGGCUG CACGCGCGCU ACACUGACUG GCUCAGCGUG UGCCUACCCU ACGCCGGCAG GCGCGGGUAA CCCGUUGAAC CCCAUUCGUG AUGGGGAUCG GGGAUUGCAA UUAUUCCCCA UGAACGAGGA AUUCCCAGUA AGUGCGGGUC AUAAGCUUGC GUUGAUUAAG UCCCUGCCCU UUGUACACAC CGCCCGUCGC UACUACCGAU UGGAUGGUUU AGUGAGGCCC UCGGAUCGGC CCCGCCGGGG UCGGCCCACG GCCCUGGCGG AGCGCUGAGA AGACGGUCGA ACUUGACUAU CUAGAGGAAG UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUAA CGG
MassTheoretical: 604.10275 kDa
SourceSpecies: Homo sapiens (human)

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Component #3: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Human (human)

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Component #4: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.538987 kDa
SourceSpecies: Human (human)

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Component #5: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.076207 kDa
SourceSpecies: Human (human)

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Component #6: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.477377 kDa
SourceSpecies: Human (human)

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Component #7: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.578156 kDa
SourceSpecies: Human (human)

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Component #8: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.759777 kDa
SourceSpecies: Human (human)

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Component #9: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.091562 kDa
SourceSpecies: Human (human)

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Component #10: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.776224 kDa
SourceSpecies: Human (human)

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Component #11: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.855052 kDa
SourceSpecies: Human (human)

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Component #12: protein, Ubiquitin-40S ribosomal protein S27a

ProteinName: Ubiquitin-40S ribosomal protein S27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.004041 kDa
SourceSpecies: Human (human)

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Component #13: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.115652 kDa
SourceSpecies: Human (human)

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Component #14: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.883938 kDa
SourceSpecies: Human (human)

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Component #15: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.002061 kDa
SourceSpecies: Human (human)

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Component #16: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.376516 kDa
SourceSpecies: Human (human)

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Component #17: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.654869 kDa
SourceSpecies: Human (human)

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Component #18: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.751906 kDa
SourceSpecies: Human (human)

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Component #19: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Human (human)

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Component #20: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.263387 kDa
SourceSpecies: Human (human)

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Component #21: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.641564 kDa
SourceSpecies: Human (human)

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Component #22: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Human (human)

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Component #23: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.259389 kDa
SourceSpecies: Human (human)

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Component #24: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.302772 kDa
SourceSpecies: Human (human)

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Component #25: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Human (human)

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Component #26: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.865555 kDa
SourceSpecies: Human (human)

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Component #27: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844666 kDa
SourceSpecies: Human (human)

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Component #28: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.463333 kDa
SourceSpecies: Human (human)

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Component #29: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.480186 kDa
SourceSpecies: Human (human)

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Component #30: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.668938 kDa
SourceSpecies: Human (human)

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Component #31: protein, RNA-binding protein PNO1

ProteinName: RNA-binding protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.970355 kDa
SourceSpecies: Human (human)

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Component #32: protein, RNA-binding protein NOB1

ProteinName: RNA-binding protein NOB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.743914 kDa
SourceSpecies: Human (human)

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Component #33: protein, Pre-rRNA-processing protein TSR1 homolog

ProteinName: Pre-rRNA-processing protein TSR1 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.951188 kDa
SourceSpecies: Human (human)

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Component #34: protein, Bystin

ProteinName: Bystin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.673258 kDa
SourceSpecies: Human (human)

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Component #35: protein, Serine/threonine-protein kinase RIO2

ProteinName: Serine/threonine-protein kinase RIO2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.372992 kDa
SourceSpecies: Human (human)

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Component #36: protein, Protein LTV1 homolog

ProteinName: Protein LTV1 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.935891 kDa
SourceSpecies: Human (human)

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Component #37: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 287847
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion 2.1
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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