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- PDB-1lqb: Crystal structure of a hydroxylated HIF-1 alpha peptide bound to ... -

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Basic information

Entry
Database: PDB / ID: 1lqb
TitleCrystal structure of a hydroxylated HIF-1 alpha peptide bound to the pVHL/elongin-C/elongin-B complex
Components
  • Elongin B
  • Elongin C
  • Hypoxia-inducible factor 1 ALPHA
  • von hippel-lindau disease tumor supressor
KeywordsGENE REGULATION / protein-peptide complex / tumor suppressor / cancer / proteosomal degradation / ubiquitin / prolyl hydroxylation
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 / positive regulation of vascular endothelial growth factor receptor signaling pathway / Replication of the SARS-CoV-1 genome / response to iron ion / Regulation of gene expression by Hypoxia-inducible Factor / VCB complex / 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 / epithelial to mesenchymal transition / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / 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 / positive regulation of chemokine production / RNA Polymerase II Transcription Elongation / 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 / protein serine/threonine kinase binding / negative regulation of autophagy / 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 / PAS fold / 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 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PAS domain / 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: 2 Å
AuthorsHon, W.C. / Wilson, M.I. / Harlos, K. / Claridge, T.D. / Schofield, C.J. / Pugh, C.W. / Maxwell, P.H. / Ratcliffe, P.J. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Nature / Year: 2002
Title: Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL.
Authors: Hon, W.C. / Wilson, M.I. / Harlos, K. / Claridge, T.D. / Schofield, C.J. / Pugh, C.W. / Maxwell, P.H. / Ratcliffe, P.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionMay 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongin B
B: Elongin C
C: von hippel-lindau disease tumor supressor
D: Hypoxia-inducible factor 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7695
Polymers46,6734
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-59 kcal/mol
Surface area18010 Å2
MethodPISA
2
A: Elongin B
B: Elongin C
C: von hippel-lindau disease tumor supressor
D: Hypoxia-inducible factor 1 ALPHA
hetero molecules

A: Elongin B
B: Elongin C
C: von hippel-lindau disease tumor supressor
D: Hypoxia-inducible factor 1 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,53810
Polymers93,3468
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area17380 Å2
ΔGint-132 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.940, 58.940, 243.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Elongin B / transcription elongation factor B / polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#2: Protein Elongin C / transcription elongation factor B (sIII) / polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 1 / Fragment: residues 17-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15369
#3: Protein von hippel-lindau disease tumor supressor / PVHL / G7 protein


Mass: 18702.291 Da / Num. of mol.: 1 / Fragment: residues 52-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40337

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Hypoxia-inducible factor 1 ALPHA / HIF-1 ALPHA


Mass: 3979.335 Da / Num. of mol.: 1 / Fragment: residues 549-582 / Source method: obtained synthetically
Details: The peptide was synthesized with a biotin tag at the N-terminus and with P564 as a 4(R)hydroxyproline. The sequence of the peptide is naturally found in homo sapiens (human).
References: UniProt: Q16665

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Non-polymers , 2 types, 85 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: HEPES, PEG2000 monomethylester, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.4
340 %PEG2000MME1reservoir
4200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2001
RadiationMonochromator: Diamond [111] and Ge crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 24245 / % possible obs: 76 % / Redundancy: 18.5 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.06 / Net I/σ(I): 20
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / Rsym value: 0.49 / % possible all: 30
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 76 % / Num. measured all: 448657 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 30 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCB.pdb

1vcb


Resolution: 2→29.26 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1108 4.8 %RANDOM
Rwork0.225 ---
obs0.225 23019 76.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5116 Å2 / ksol: 0.341289 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 5 84 2994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 102 4.9 %
Rwork0.289 1978 -
obs-1546 42.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_HYP.PARWATER.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN_HYP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor obs: 0.225 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Lowest resolution: 2.07 Å / Rfactor Rfree: 0.352 / Rfactor Rwork: 0.289

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