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- PDB-1lm8: Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex -

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Basic information

Entry
Database: PDB / ID: 1lm8
TitleStructure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
Components
  • ELONGIN B
  • ELONGIN C
  • 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 / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / hemoglobin biosynthetic process / negative regulation of mesenchymal cell apoptotic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / negative regulation of growth / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / retina vasculature development in camera-type eye / mesenchymal cell apoptotic process / regulation of protein neddylation / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / B-1 B cell homeostasis / collagen metabolic process / vascular endothelial growth factor production / regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / dopaminergic neuron differentiation / transcription regulator activator activity / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / STAT3 nuclear events downstream of ALK signaling / lactate metabolic process / negative regulation of thymocyte apoptotic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / Replication of the SARS-CoV-1 genome / positive regulation of vascular endothelial growth factor receptor signaling pathway / response to iron ion / VCB complex / Regulation of gene expression by Hypoxia-inducible Factor / neural crest cell migration / embryonic hemopoiesis / Cul5-RING ubiquitin ligase complex / regulation of glycolytic process / motile cilium / DNA-binding transcription repressor activity / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / digestive tract morphogenesis / SUMOylation of ubiquitinylation proteins / response to muscle activity / axonal transport of mitochondrion / heart looping / bone mineralization / intracellular glucose homeostasis / E-box binding / TOR signaling / outflow tract morphogenesis / positive regulation of vascular endothelial growth factor production / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / positive regulation of macroautophagy / positive regulation of epithelial cell migration / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / epithelial to mesenchymal transition / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / chondrocyte differentiation / embryonic placenta development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / cis-regulatory region sequence-specific DNA binding / RNA Polymerase II Transcription Elongation / positive regulation of chemokine production / Formation of RNA Pol II elongation complex / lactation / negative regulation of TORC1 signaling / positive regulation of endothelial cell proliferation / RNA Polymerase II Pre-transcription Events / axon cytoplasm / negative regulation of autophagy / protein serine/threonine kinase binding / negative regulation of miRNA transcription
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 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 ...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 1-alpha bHLH 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-C / Elongin B / 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / PAS repeat profile. / PAS domain / PAS domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein ELONGIN B


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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