[English] 日本語
Yorodumi
- PDB-1lqb: Crystal structure of a hydroxylated HIF-1 alpha peptide bound to ... -

+
Open data


ID or keywords:

Loading...

-
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


elastin metabolic process / positive regulation of chemokine-mediated signaling pathway / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / collagen metabolic process / PTK6 Expression / regulation of protein neddylation / vascular endothelial growth factor production ...elastin metabolic process / positive regulation of chemokine-mediated signaling pathway / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / collagen metabolic process / PTK6 Expression / regulation of protein neddylation / vascular endothelial growth factor production / regulation of cellular response to hypoxia / intracellular oxygen homeostasis / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / negative regulation of ossification / transcription regulator activator activity / STAT3 nuclear events downstream of ALK signaling / target-directed miRNA degradation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / elongin complex / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / Replication of the SARS-CoV-1 genome / Regulation of gene expression by Hypoxia-inducible Factor / response to iron ion / transcription elongation factor activity / positive regulation of cytokine production involved in inflammatory response / regulation of glycolytic process / DNA-binding transcription repressor activity / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / SUMOylation of ubiquitinylation proteins / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / negative regulation of transcription elongation by RNA polymerase II / axonal transport of mitochondrion / E-box binding / positive regulation of epithelial cell migration / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cellular response to interleukin-1 / epithelial to mesenchymal transition / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of vascular endothelial growth factor production / positive regulation of blood vessel endothelial cell migration / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / cell morphogenesis / Formation of HIV elongation complex in the absence of HIV Tat / cis-regulatory region sequence-specific DNA binding / ubiquitin-like ligase-substrate adaptor activity / positive regulation of chemokine production / RNA Polymerase II Transcription Elongation / negative regulation of reactive oxygen species biosynthetic process / Formation of RNA Pol II elongation complex / ribosome-associated ubiquitin-dependent protein catabolic process / positive regulation of endothelial cell proliferation / negative regulation of TORC1 signaling / axon cytoplasm / positive regulation of erythrocyte differentiation / RNA Polymerase II Pre-transcription Events / negative regulation of miRNA transcription / intracellular glucose homeostasis / positive regulation of glycolytic process / negative regulation of autophagy / nuclear receptor binding / transcription corepressor binding / response to reactive oxygen species / protein serine/threonine kinase binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / cellular response to virus / transcription initiation at RNA polymerase II promoter / euchromatin / Hsp90 protein binding / transcription elongation by RNA polymerase II / positive regulation of miRNA transcription / Inactivation of CSF3 (G-CSF) signaling / Vif-mediated degradation of APOBEC3G / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / transcription coactivator binding / histone deacetylase binding / positive regulation of angiogenesis / Regulation of expression of SLITs and ROBOs / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / p53 binding / ubiquitin-protein transferase activity / transcription corepressor activity / regulation of gene expression / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PD-L1(CD274) 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Elongin-C / Elongin B / 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 / PAS repeat profile. / PAS domain / SKP1/BTB/POZ domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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 (eV)
18 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.4
340 %PEG2000MME1reservoir
4200 mMammonium sulfate1reservoir

-
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

-
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

+
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