[English] 日本語
Yorodumi
- PDB-4awj: pVHL:EloB:EloC complex, in complex with capped Hydroxyproline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4awj
TitlepVHL:EloB:EloC complex, in complex with capped Hydroxyproline
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsTRANSCRIPTION / E3 UBIQUITIN LIGASE / TUMOR SUPRESSOR
Function / homology
Function and homology information


regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / transcription elongation factor activity / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway ...regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / transcription elongation factor activity / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / 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 / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / ciliary tip / transcription corepressor binding / negative regulation of autophagy / protein serine/threonine kinase binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / DNA-binding transcription factor binding / molecular adaptor activity / amyloid fibril formation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / protein stabilization / cilium / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ 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
ACETATE ION / ACETIC ACID / (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsVan Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A.
CitationJournal: Chem.Biol. / Year: 2012
Title: Dissecting Fragment-Based Lead Discovery at the Von Hippel-Lindau Protein:Hypoxia Inducible Factor 1Alpha Protein-Protein Interface.
Authors: Van Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A.
History
DepositionJun 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
D: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
G: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
H: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
I: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
J: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
K: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
L: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,75324
Polymers167,50212
Non-polymers1,25112
Water5,206289
1
A: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
C: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2397
Polymers41,8753
Non-polymers3634
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-38.7 kcal/mol
Surface area15490 Å2
MethodPISA
2
D: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
E: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
F: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1816
Polymers41,8753
Non-polymers3053
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-32.2 kcal/mol
Surface area15840 Å2
MethodPISA
3
G: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
H: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
I: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1215
Polymers41,8753
Non-polymers2452
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-40.4 kcal/mol
Surface area16260 Å2
MethodPISA
4
J: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
K: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
L: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2136
Polymers41,8753
Non-polymers3373
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-40.7 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 93.400, 362.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

-
Components

-
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / ELONGIN 18 KDA SUBUNIT / ELONGIN-B / ELOB / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18


Mass: 11956.372 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#2: Protein
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 / ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15


Mass: 10974.616 Da / Num. of mol.: 4 / Fragment: RESIDUES 17-112
Source method: isolated from a genetically manipulated source
Details: EXTRA M AT N-TERMINUS AS RESULT OF CLONING / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369

-
Protein , 1 types, 4 molecules CFIL

#3: Protein
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR / PROTEIN G7 / PVHL


Mass: 18944.420 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337

-
Non-polymers , 5 types, 301 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-V6F / (4R)-1-acetyl-4-hydroxy-N-methyl-L-prolinamide


Mass: 186.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14N2O3
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer details3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (V6F): CAPPED HYDROXYPROLINE
Sequence detailsGSH REMAINING AFTER THROMBIN CLEAVAGE EXTRA M AT N-TERMINUS AS RESULT OF CLONING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.31 % / Description: NONE
Crystal growpH: 6
Details: 0.1 M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 28, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 56728 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 12.6 % / Biso Wilson estimate: 46.53 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.34
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.25 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→29.536 Å / SU ML: 0.41 / σ(F): 2.01 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 2834 5 %
Rwork0.2202 --
obs0.2224 56672 99.89 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.169 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.6276 Å20 Å20 Å2
2--13.6276 Å20 Å2
3---4.2148 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10389 0 86 289 10764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210721
X-RAY DIFFRACTIONf_angle_d0.63414573
X-RAY DIFFRACTIONf_dihedral_angle_d12.6043971
X-RAY DIFFRACTIONf_chiral_restr0.0441666
X-RAY DIFFRACTIONf_plane_restr0.0031888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.37181390.32182640X-RAY DIFFRACTION100
2.5431-2.58930.42161400.30962645X-RAY DIFFRACTION100
2.5893-2.63910.37921380.2972628X-RAY DIFFRACTION100
2.6391-2.69290.32811390.2812648X-RAY DIFFRACTION100
2.6929-2.75140.33331420.26022685X-RAY DIFFRACTION100
2.7514-2.81540.28251370.25252611X-RAY DIFFRACTION100
2.8154-2.88570.34191390.25162645X-RAY DIFFRACTION100
2.8857-2.96370.30661390.23712630X-RAY DIFFRACTION100
2.9637-3.05080.30821410.2432674X-RAY DIFFRACTION100
3.0508-3.14920.27731400.24362673X-RAY DIFFRACTION100
3.1492-3.26160.26861410.23282670X-RAY DIFFRACTION100
3.2616-3.3920.32931400.23612659X-RAY DIFFRACTION100
3.392-3.54610.26531410.23032688X-RAY DIFFRACTION100
3.5461-3.73270.27481420.2242706X-RAY DIFFRACTION100
3.7327-3.96610.22631410.20842679X-RAY DIFFRACTION100
3.9661-4.27150.23231440.18472730X-RAY DIFFRACTION100
4.2715-4.69980.20161430.16252725X-RAY DIFFRACTION100
4.6998-5.37630.22191450.18482748X-RAY DIFFRACTION100
5.3763-6.76020.26461480.23762807X-RAY DIFFRACTION100
6.7602-29.53770.22051550.20542947X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.7793 Å / Origin y: 30.0951 Å / Origin z: 23.9475 Å
111213212223313233
T0.2767 Å2-0.0455 Å20.1282 Å2--0.2 Å20.1153 Å2--0.0383 Å2
L0.0427 °2-0.0096 °20.0549 °2-0.1008 °20.002 °2---0.0299 °2
S0.004 Å °-0.004 Å °-0.0083 Å °-0.0796 Å °-0.0517 Å °0.0263 Å °0.0128 Å °-0.036 Å °0.0051 Å °
Refinement TLS groupSelection details: ALL

+
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