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- PDB-9ndp: Structure of stalled ribosome and nascent chain in complex with N... -

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Basic information

Entry
Database: PDB / ID: 9ndp
TitleStructure of stalled ribosome and nascent chain in complex with NMT2 and NAC
Components
  • (40S ribosomal protein ...) x 7
  • (60S ribosomal protein ...) x 13
  • (Large ribosomal subunit protein ...) x 6
  • (Ribosomal protein ...) x 17
  • (Small ribosomal subunit protein ...) x 5
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • Glycylpeptide N-tetradecanoyltransferase 2
  • Isoform 2 of Transcription factor BTF3
  • Myristoylated alanine-rich C-kinase substrate,X-box-binding protein 1, luminal form
  • Nascent polypeptide-associated complex subunit alpha
  • RACK1
  • S10_plectin domain-containing protein
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • eL13
  • eL21
  • eL22
  • eL23
  • eL24
  • eL28
  • eL30
  • eL31
  • eL33
  • eL35
  • eL39
  • eL41
  • eL43
  • eS17
  • eS19
  • eS25
  • eS29
  • eS4
  • mRNA
  • tRNA
  • uL24
  • uS10
  • uS12
  • uS13
  • uS19
  • uS2 (SA)
  • uS9
KeywordsRIBOSOME / protein synthesis / N-glycine myristoylation / NMT2 / NAC
Function / homology
Function and homology information


postsynaptic cytoskeleton / Acetylcholine regulates insulin secretion / epithelial cell maturation involved in salivary gland development / organelle / positive regulation of vascular wound healing / ATF6-mediated unfolded protein response / positive regulation of protein acetylation / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / outer dense fiber ...postsynaptic cytoskeleton / Acetylcholine regulates insulin secretion / epithelial cell maturation involved in salivary gland development / organelle / positive regulation of vascular wound healing / ATF6-mediated unfolded protein response / positive regulation of protein acetylation / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / outer dense fiber / negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / intracellular transport of virus / positive regulation of cell proliferation involved in heart morphogenesis / response to insulin-like growth factor stimulus / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of skeletal muscle tissue growth / glandular epithelial cell maturation / positive regulation of lactation / sterol homeostasis / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of plasma cell differentiation / regulation of opsin-mediated signaling pathway / positive regulation of phospholipid biosynthetic process / cardiac ventricle development / negative regulation of myotube differentiation / positive regulation of ERAD pathway / intracellular triglyceride homeostasis / actin crosslink formation / ventricular cardiac muscle tissue development / bleb / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cellular response to fructose stimulus / chromatoid body / cellular response to laminar fluid shear stress / regulation of modification of postsynaptic actin cytoskeleton / XBP1(S) activates chaperone genes / positive regulation of dendritic spine morphogenesis / heart trabecula morphogenesis / cellular response to nutrient / skeletal muscle tissue regeneration / positive regulation of hepatocyte proliferation / dendritic branch / cellular response to fluid shear stress / positive regulation of MHC class II biosynthetic process / negative regulation of endoplasmic reticulum unfolded protein response / exocrine pancreas development / positive regulation of vascular associated smooth muscle cell migration / germinal vesicle / ribosomal subunit / endothelial cell proliferation / protein localization to membrane / neural tube development / cellular response to peptide hormone stimulus / positive regulation of B cell differentiation / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / muscle organ development / IRE1-mediated unfolded protein response / phosphatidylserine binding / cell-substrate adhesion / actin filament bundle / negative regulation of SMAD protein signal transduction / actin filament bundle assembly / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to vascular endothelial growth factor stimulus / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling / 90S preribosome / positive regulation of insulin receptor signaling pathway / adipose tissue development / fatty acid homeostasis / vascular endothelial growth factor receptor signaling pathway / positive regulation of fat cell differentiation / neuron development / phagocytic cup / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / presynaptic cytosol / ribosomal small subunit export from nucleus / positive regulation of vascular associated smooth muscle cell proliferation / rough endoplasmic reticulum / translation regulator activity / eNOS activation / gastrulation / ERAD pathway / neurogenesis / MDM2/MDM4 family protein binding / axon terminus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Membrane binding and targetting of GAG proteins / positive regulation of autophagy / cytosolic ribosome
Similarity search - Function
Myristoylated alanine-rich C-kinase substrate MARCKS / MARCKS family / MARCKS family signature 1. / MARCKS family phosphorylation site domain. / : / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain ...Myristoylated alanine-rich C-kinase substrate MARCKS / MARCKS family / MARCKS family signature 1. / MARCKS family phosphorylation site domain. / : / Transcription factor BTF3 / Nascent polypeptide-associated complex NAC domain / Nascent polypeptide-associated complex subunit alpha / NAC A/B domain superfamily / NAC domain / NAC A/B domain profile. / NAC / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / S27a-like superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S30 / Ribosomal protein S17e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 1. / Ribosomal L40e family / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L36e signature. / Ribosomal protein L35Ae, conserved site / :
Similarity search - Domain/homology
COENZYME A / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS24 / Ribosomal protein L36a / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 ...COENZYME A / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein eS24 / Ribosomal protein L36a / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L32 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Glycylpeptide N-tetradecanoyltransferase 2 / Ubiquitin-ribosomal protein eL40 fusion protein / X-box-binding protein 1 / Large ribosomal subunit protein uL18 / Transcription factor BTF3 / Myristoylated alanine-rich C-kinase substrate / Nascent polypeptide-associated complex subunit alpha / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsZdancewicz, S. / Jomaa, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: EMBO J / Year: 2025
Title: NAC couples protein synthesis with nascent polypeptide myristoylation on the ribosome.
Authors: Sara Zdancewicz / Emir Maldosevic / Kinga Malezyna / Ahmad Jomaa /
Abstract: N-glycine myristoylation allows for reversible association of newly synthesized proteins with membranes to regulate essential functions such as cellular signaling and stress responses. This process ...N-glycine myristoylation allows for reversible association of newly synthesized proteins with membranes to regulate essential functions such as cellular signaling and stress responses. This process can be catalyzed during protein synthesis by N-myristoyltransferases (NMTs), and its dysregulation has been implicated both in cancer and heart disease. Although the nascent polypeptide-associated complex (NAC) orchestrates the binding of several co-translational processing factors on ribosomes, its role in facilitating nascent protein myristoylation by NMT2 remains unclear. Here, we show that NAC mediates binding of NMT2 to translating ribosomes, which together form an extended channel that guides the nascent chain as it emerges from the polypeptide exit tunnel to the catalytic site of NMT2. Furthermore, the ternary ribosome:NMT2:NAC complex is stabilized by a ribosomal RNA clamp that, together with NAC, orients NMT2 on the ribosomal surface for co-translational myristoylation of nascent chains. Our work uncovers the molecular mechanism coupling protein synthesis to nascent protein myristoylation and underscores the role of NAC as a master regulator of protein biogenesis on the ribosome.
History
DepositionFeb 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Ribosomal protein S27a
4: mRNA
6: RACK1
7: 5S rRNA
9: eS29
A: Ribosomal protein L8
B: Ribosomal protein L3
C: 60S ribosomal protein L4
D: Large ribosomal subunit protein uL18
F: Large ribosomal subunit protein uL30
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: Ribosomal protein L11
K: 18S rRNA
L: eL13
M: 60S ribosomal protein L14
N: Ribosomal protein L15
O: Large ribosomal subunit protein uL13
P: Large ribosomal subunit protein uL22
Q: Ribosomal protein L18
R: Ribosomal protein L19
S: 60S ribosomal protein L18a
T: eL21
U: eL22
V: Ribosomal protein L23
W: eL24
X: eL23
Y: uL24
Z: 60S ribosomal protein L27
a: 60S ribosomal protein L27a
c: eL30
d: eL31
e: 60S ribosomal protein L32
f: eL33
g: 60S ribosomal protein L34
h: eL35
i: 60S ribosomal protein L36
j: Ribosomal protein L37
k: Large ribosomal subunit protein eL38
l: eL39
m: Ubiquitin-ribosomal protein eL40 fusion protein
n: eL41
o: Ribosomal protein L36a
p: eL43
q: uS2 (SA)
r: eL28
u: 40S ribosomal protein S3a
v: Small ribosomal subunit protein uS5
w: Ribosomal protein S3
x: eS4
z: 40S ribosomal protein S6
s: 60S acidic ribosomal protein P0
t: 60S ribosomal protein L12
2: tRNA
5: 28S rRNA
8: 5.8S rRNA
E: 60S ribosomal protein L6
b: Large ribosomal subunit protein eL29
y: Ribosomal protein S5
BB: 40S ribosomal protein S7
CC: 40S ribosomal protein S8
DD: Ribosomal protein S9 (Predicted)
SS: S10_plectin domain-containing protein
EE: Ribosomal protein S11
RR: 40S ribosomal protein S12
QQ: Ribosomal protein S13
MM: Small ribosomal subunit protein uS11
WW: uS19
UU: uS9
KK: eS17
II: uS13
PP: eS19
GG: uS10
HH: Small ribosomal subunit protein eS21
TT: Ribosomal protein S15a
VV: uS12
NN: Small ribosomal subunit protein eS24
OO: eS25
LL: Small ribosomal subunit protein eS26
JJ: 40S ribosomal protein S27
FF: Ribosomal protein S28
AA: 40S ribosomal protein S30
EF: Isoform 2 of Transcription factor BTF3
EG: Nascent polypeptide-associated complex subunit alpha
NA: Glycylpeptide N-tetradecanoyltransferase 2
NB: Myristoylated alanine-rich C-kinase substrate,X-box-binding protein 1, luminal form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,443,233390
Polymers3,434,87987
Non-polymers8,354303
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Ribosomal protein ... , 17 types, 17 molecules 0ABJNQRVjowyDDEEQQTTFF

#1: Protein Ribosomal protein S27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#6: Protein Ribosomal protein L8


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#7: Protein Ribosomal protein L3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#14: Protein Ribosomal protein L11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#18: Protein Ribosomal protein L15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#21: Protein Ribosomal protein L18


Mass: 21721.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein Ribosomal protein L19


Mass: 21715.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein Ribosomal protein L23


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#39: Protein Ribosomal protein L37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#44: Protein Ribosomal protein L36a


Mass: 16130.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D391
#50: Protein Ribosomal protein S3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#60: Protein Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#63: Protein Ribosomal protein S9 (Predicted)


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#65: Protein Ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#67: Protein Ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#76: Protein Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#82: Protein Ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4

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RNA chain , 6 types, 6 molecules 47K258

#2: RNA chain mRNA


Mass: 1877.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: RNA chain 5S rRNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: RNA chain 18S rRNA


Mass: 548040.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: RNA chain tRNA


Mass: 24414.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#56: RNA chain 28S rRNA


Mass: 1145287.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: RNA chain 5.8S rRNA


Mass: 48545.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 32 types, 32 molecules 69LTUWXYcdfhlmpqrxsSSWWUUKKIIPPGGVVOOEFEGNANB

#3: Protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#5: Protein eS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#16: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#24: Protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#25: Protein eL22


Mass: 13322.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#28: Protein eL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#29: Protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#32: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#33: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#35: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#37: Protein eL35


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#41: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#42: Protein Ubiquitin-ribosomal protein eL40 fusion protein / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P0DXC2
#45: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#46: Protein uS2 (SA)


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#47: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#51: Protein eS4 / 40S ribosomal protein S4


Mass: 29596.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#53: Protein 60S acidic ribosomal protein P0


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#64: Protein S10_plectin domain-containing protein


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#69: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#70: Protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#71: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#72: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#73: Protein eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#74: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#77: Protein uS12 / 40S ribosomal protein S23


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#79: Protein eS25 / 40S ribosomal protein S25


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#84: Protein Isoform 2 of Transcription factor BTF3 / Nascent polypeptide-associated complex subunit beta / NAC-beta / RNA polymerase B transcription factor 3


Mass: 17724.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTF3, NACB, OK/SW-cl.8 / Production host: Escherichia coli (E. coli) / References: UniProt: P20290
#85: Protein Nascent polypeptide-associated complex subunit alpha / NAC-alpha / Alpha-NAC


Mass: 23406.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NACA, HSD48 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13765
#86: Protein Glycylpeptide N-tetradecanoyltransferase 2 / Myristoyl-CoA:protein N-myristoyltransferase 2 / NMT 2 / Peptide N-myristoyltransferase 2 / Protein- ...Myristoyl-CoA:protein N-myristoyltransferase 2 / NMT 2 / Peptide N-myristoyltransferase 2 / Protein-lysine myristoyltransferase NMT2 / Type II N-myristoyltransferase


Mass: 57061.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: O60551, glycylpeptide N-tetradecanoyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#87: Protein Myristoylated alanine-rich C-kinase substrate,X-box-binding protein 1, luminal form / MARCKS / Protein kinase C substrate 80 kDa protein


Mass: 7682.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The listed sample sequence is not correct! Please update! The full sample sequence should be "GAQFSKTAAKGEAAAERPGEAAVASSPSKANGQENGHVKVNGDASPAAAEDPVPYQPPFLCQWGRHQCAWKPLM" but the software ...Details: The listed sample sequence is not correct! Please update! The full sample sequence should be "GAQFSKTAAKGEAAAERPGEAAVASSPSKANGQENGHVKVNGDASPAAAEDPVPYQPPFLCQWGRHQCAWKPLM" but the software will not properly align the first 9 residues and the final residues with such a large gap in between. I deleted 31 residues from the middle of the sequence to get the system to accept this,The listed sample sequence is not correct! Please update! The full sample sequence should be "GAQFSKTAAKGEAAAERPGEAAVASSPSKANGQENGHVKVNGDASPAAAEDPVPYQPPFLCQWGRHQCAWKPLM" but the software will not properly align the first 9 residues and the final residues with such a large gap in between. I deleted 31 residues from the middle of the sequence to get the system to accept this
Source: (gene. exp.) Homo sapiens (human) / Gene: Marcks, Macs, XBP1, TREB5, XBP2 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: P30009, UniProt: P17861

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60S ribosomal protein ... , 13 types, 13 molecules CGHIMSZaegitE

#8: Protein 60S ribosomal protein L4


Mass: 46388.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#11: Protein 60S ribosomal protein L7a


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#12: Protein 60S ribosomal protein L9


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#13: Protein 60S ribosomal protein L10 / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#17: Protein 60S ribosomal protein L14


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#23: Protein 60S ribosomal protein L18a


Mass: 20661.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#30: Protein 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#31: Protein 60S ribosomal protein L27a


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#34: Protein 60S ribosomal protein L32


Mass: 15767.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAG1WVT3
#36: Protein 60S ribosomal protein L34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#38: Protein 60S ribosomal protein L36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#54: Protein 60S ribosomal protein L12


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#58: Protein 60S ribosomal protein L6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7

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Large ribosomal subunit protein ... , 6 types, 6 molecules DFOPkb

#9: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P19949
#10: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 29514.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAG1W3S3
#19: Protein Large ribosomal subunit protein uL13 / 60S ribosomal protein L13a


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVS8
#20: Protein Large ribosomal subunit protein uL22 / 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SCJ6
#40: Protein Large ribosomal subunit protein eL38


Mass: 12047.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#59: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29


Mass: 26708.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6

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Protein/peptide , 1 types, 1 molecules n

#43: Protein/peptide eL41 / 60s ribosomal protein l41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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40S ribosomal protein ... , 7 types, 7 molecules uzBBCCRRJJAA

#48: Protein 40S ribosomal protein S3a


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#52: Protein 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#61: Protein 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#62: Protein 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#66: Protein 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#81: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#83: Protein 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2

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Small ribosomal subunit protein ... , 5 types, 5 molecules vMMHHNNLL

#49: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 27502.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0AAG1W6H3
#68: Protein Small ribosomal subunit protein uS11 / 40S ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#75: Protein Small ribosomal subunit protein eS21


Mass: 9074.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9D2E6
#80: Protein Small ribosomal subunit protein eS26


Mass: 13147.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Non-polymers , 3 types, 303 molecules

#88: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 296 / Source method: obtained synthetically / Formula: Mg
#89: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#90: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
180S Ribosome containing MARCKS-Xbp1 chimeric nascent chainRIBOSOME80S ribosome purified from rabbit reticulocyte lysate and containing a nascent polypeptide with the N-terminal of MARCKS and stalled using an Xbp1 stalling sequence#1-#47, #53-#54, #48-#52, #55-#850NATURAL
2ribosome bound nascent polypeptide associated complexCOMPLEXheterodimeric protein NAC recombinantly expressed and purified#84-#851RECOMBINANT
3ribosome bound N-myristoyltransferase 2COMPLEXenzyme responsible for myristoylation of nascent chains on the ribosome#861RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oryctolagus cuniculus (rabbit)9986
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23479 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002234192
ELECTRON MICROSCOPYf_angle_d0.425343079
ELECTRON MICROSCOPYf_dihedral_angle_d14.433106522
ELECTRON MICROSCOPYf_chiral_restr0.02942590
ELECTRON MICROSCOPYf_plane_restr0.00322667

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