[English] 日本語
Yorodumi
- PDB-1lm8: Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lm8
TitleStructure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
Components
  • ELONGIN BELOB
  • ELONGIN CELOC
  • Hypoxia-inducible factor 1 alpha
  • Von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / REGULATION / tumor suppressor / oxygen sensing
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / retina vasculature development in camera-type eye / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / collagen metabolic process / positive regulation of mitophagy / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / negative regulation of bone mineralization / regulation of cellular response to hypoxia / PTK6 Expression / lactate metabolic process / intracellular oxygen homeostasis / B-1 B cell homeostasis / vascular endothelial growth factor production / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / negative regulation of TOR signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / transcription regulator activator activity / dopaminergic neuron differentiation / STAT3 nuclear events downstream of ALK signaling / target-directed miRNA degradation / elongin complex / VCB complex / positive regulation of cytokine production involved in inflammatory response / motile cilium / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / response to muscle activity / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / neural crest cell migration / embryonic hemopoiesis / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Cul2-RING ubiquitin ligase complex / muscle cell cellular homeostasis / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of neuroblast proliferation / intracellular non-membrane-bounded organelle / axonal transport of mitochondrion / SUMOylation of ubiquitinylation proteins / positive regulation of epithelial cell migration / heart looping / bone mineralization / TOR signaling / E-box binding / outflow tract morphogenesis / negative regulation of transcription elongation by RNA polymerase II / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / neuroblast proliferation / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / Tat-mediated elongation of the HIV-1 transcript / positive regulation of blood vessel endothelial cell migration / Formation of HIV-1 elongation complex containing HIV-1 Tat / cellular response to interleukin-1 / chondrocyte differentiation / cis-regulatory region sequence-specific DNA binding / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / axon cytoplasm / positive regulation of chemokine production / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / lactation / positive regulation of endothelial cell proliferation / positive regulation of glycolytic process
Similarity search - Function
Hypoxia-inducible factor-1 alpha / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain ...Hypoxia-inducible factor-1 alpha / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / PAS fold / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B / Hypoxia-inducible factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMin, J.-H. / Yang, H. / Ivan, M. / Gertler, F. / Kaelin JR., W.G. / Pavletich, N.P.
CitationJournal: Science / Year: 2002
Title: Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling.
Authors: Min, J.H. / Yang, H. / Ivan, M. / Gertler, F. / Kaelin Jr., W.G. / Pavletich, N.P.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: ELONGIN B
C: ELONGIN C
V: Von Hippel-Lindau disease tumor suppressor
H: Hypoxia-inducible factor 1 alpha


Theoretical massNumber of molelcules
Total (without water)44,9774
Polymers44,9774
Non-polymers00
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-49 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.5, 59.5, 245.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ELONGIN B / ELOB


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: Protein ELONGIN C / ELOC


Mass: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein Von Hippel-Lindau disease tumor suppressor / VHL


Mass: 18558.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#4: Protein/peptide Hypoxia-inducible factor 1 alpha / HIF-1 alpha / ARNT interacting protein / MOP1


Mass: 2427.726 Da / Num. of mol.: 1 / Fragment: Residues 556-575 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo sapiens.
References: UniProt: Q16665
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
121 mg/mlprotein1drop
25 mMBis-Tris propane1droppH7.0
3200 mM1dropNaCl
45 mMdithiothreitol1drop
524 %(w/v)PME50001reservoir
60.1 Mpotassium phosphate1reservoirpH6.5
70.2 Mammonium sulfate1reservoir
85 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 38461 / Num. obs: 34115 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.382 / % possible all: 76.5
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 248351 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 76.5 % / Rmerge(I) obs: 0.382

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VCB

1vcb


Resolution: 1.85→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1360 5 %random
Rwork0.196 ---
all-38866 --
obs-33935 87.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.853 Å2--
2--0.853 Å2-
3----1.706 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 0 523 3406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.196 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.92 Å / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.248 / Rfactor obs: 0.248

+
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://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