[English] 日本語
Yorodumi
- PDB-7tbh: cryo-EM structure of MBP-KIX-apoferritin complex with peptide 7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tbh
Titlecryo-EM structure of MBP-KIX-apoferritin complex with peptide 7
Components
  • Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
  • LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
KeywordsSTRUCTURAL PROTEIN / Protein Engineering / Simulation / Peptide Therapeutics / Acute Myeloid Leukemia
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / iron ion sequestering activity ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / iron ion sequestering activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / autolysosome / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / ferroxidase / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / intracellular sequestering of iron ion / ferroxidase activity / Attenuation phase / regulation of cellular response to heat / negative regulation of fibroblast proliferation / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / endocytic vesicle lumen / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / Neutrophil degranulation / CD209 (DC-SIGN) signaling / ferric iron binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / ferrous iron binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Evasion by RSV of host interferon responses / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / iron ion transport / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / transcription coactivator activity / nuclear body / response to hypoxia / iron ion binding
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Nuclear receptor coactivator, interlocking / Ferritin-like / Ferritin-like superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ferritin heavy chain / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsZhang, K. / Horikoshi, N. / Li, S. / Powers, A. / Hameedi, M. / Pintilie, G. / Chae, H. / Khan, Y. / Suomivuori, C. / Dror, R. ...Zhang, K. / Horikoshi, N. / Li, S. / Powers, A. / Hameedi, M. / Pintilie, G. / Chae, H. / Khan, Y. / Suomivuori, C. / Dror, R. / Sakamoto, K. / Chiu, W. / Wakatsuki, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021600 United States
CitationJournal: ACS Cent Sci / Year: 2022
Title: Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia.
Authors: Kaiming Zhang / Naoki Horikoshi / Shanshan Li / Alexander S Powers / Mikhail A Hameedi / Grigore D Pintilie / Hee-Don Chae / Yousuf A Khan / Carl-Mikael Suomivuori / Ron O Dror / Kathleen M ...Authors: Kaiming Zhang / Naoki Horikoshi / Shanshan Li / Alexander S Powers / Mikhail A Hameedi / Grigore D Pintilie / Hee-Don Chae / Yousuf A Khan / Carl-Mikael Suomivuori / Ron O Dror / Kathleen M Sakamoto / Wah Chiu / Soichi Wakatsuki /
Abstract: Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures ...Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target-apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix-helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors.
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-25799
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-25799
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
B: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
C: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
D: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
E: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
F: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
G: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
H: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
I: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
J: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
K: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
L: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
M: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
N: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
O: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
P: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
Q: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
R: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
S: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
T: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
U: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
V: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
W: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
X: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed
a: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
b: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
c: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
d: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
e: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
f: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
g: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
h: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
i: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
j: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
k: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
l: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
m: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
n: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
o: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
p: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
q: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
r: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
s: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
t: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
u: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
v: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
w: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO
x: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO


Theoretical massNumber of molelcules
Total (without water)784,34148
Polymers784,34148
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed / Histone lysine acetyltransferase CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 30408.438 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP, Fth1, Fth
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q92793, UniProt: P09528, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide ...
LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO


Mass: 2272.457 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: MBP-KIX-apoferritin complex with peptide 7 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: MBP-KIX-apoferritin complex with peptide 7
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 43.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2490
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1EMAN22.3particle selection
2EPU2.7image acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.41model fitting
9PHENIXmodel refinement
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 124114
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35613 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Target criteria: Q-score

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more