[English] 日本語
Yorodumi
- PDB-6yw4: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylgl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yw4
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Components
  • Egl nine homolog 1
  • PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / heart trabecula formation ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / negative regulation of DNA-binding transcription factor activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 Å
AuthorsChowdhury, R. / Schofield, C.J.
Citation
Journal: Sci Rep / Year: 2020
Title: Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Authors: Chowdhury, R. / Abboud, M.I. / McAllister, T.E. / Banerji, B. / Bhushan, B. / Sorensen, J.L. / Kawamura, A. / Schofield, C.J.
#1: Journal: Nat Commun / Year: 2016
Title: Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.
Authors: Chowdhury, R. / Leung, I.K. / Tian, Y.M. / Abboud, M.I. / Ge, W. / Domene, C. / Cantrelle, F.X. / Landrieu, I. / Hardy, A.P. / Pugh, C.W. / Ratcliffe, P.J. / Claridge, T.D. / Schofield, C.J.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Egl nine homolog 1
B: PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1146
Polymers27,7192
Non-polymers3944
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-43 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.622, 46.622, 203.711
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing ...Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 25918.402 Da / Num. of mol.: 1 / Mutation: C201A/R398A
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (aa 181-407) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Protein/peptide PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)


Mass: 1801.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 197 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), protein-to-well ratio, 1:1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.528→50 Å / Num. obs: 37807 / % possible obs: 100 % / Redundancy: 16 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.039 / Rrim(I) all: 0.129 / Χ2: 1.043 / Net I/σ(I): 20.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.53-1.5813.11.7331240.6530.5321.104100
1.58-1.6316.131700.7050.4981.099100
1.63-1.6815.731340.7810.4011.073100
1.68-1.7516.731290.9040.2641.065100
1.75-1.8317.331320.9330.1981.0411000.8140.838
1.83-1.931731550.9660.1321.0261000.5340.55
1.93-2.0516.431420.9790.0951.0171000.3760.388
2.05-2.2117.731620.9880.0661.0141000.2680.276
2.21-2.4317.331400.9940.0491.0241000.1970.203
2.43-2.7816.331560.9950.0371.00799.90.1450.15
2.78-3.515.531540.9970.0261.0341000.0960.099
3.5-5013.132090.9960.021.02299.90.0710.074

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9R

5l9r


Resolution: 1.528→39.605 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1841 4.89 %
Rwork0.162 --
obs0.1628 37652 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 50.2 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 118.95 Å2 / Biso mean: 34.4686 Å2 / Biso min: 15 Å2
Refinement stepCycle: final / Resolution: 1.528→39.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 24 193 1973
Biso mean--54.01 40.69 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0160.1271854
X-RAY DIFFRACTIONf_angle_d1.40710.5082513
X-RAY DIFFRACTIONf_dihedral_angle_d11.882160.6331081
X-RAY DIFFRACTIONf_chiral_restr0.0870.295264
X-RAY DIFFRACTIONf_plane_restr0.0120.06326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.528-1.56920.28221210.2731270598
1.5692-1.61530.28281390.24722814100
1.6153-1.66750.25211420.23052759100
1.6675-1.72710.26261570.19982743100
1.7271-1.79620.22011200.18752774100
1.7962-1.8780.19991370.16132740100
1.878-1.9770.17281620.15072730100
1.977-2.10080.18251300.15262775100
2.1008-2.2630.16441260.14432770100
2.263-2.49080.18261660.1442725100
2.4908-2.85110.16751400.15042764100
2.8511-3.59170.151450.15772761100
3.5917-39.6050.16821560.15972751100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01430.03020.03650.13490.11531.2422-0.0884-0.0224-0.2097-0.0752-0.02320.0529-0.1132-0.5336-0.02760.11380.0076-0.00340.3986-0.00350.2799-31.034211.1408-3.3499
20.0144-0.0663-0.01090.4176-0.06150.10950.0101-0.2219-0.0642-0.14410.09040.2960.0275-0.31960.00660.13930.02980.00820.27160.01270.1862-22.462710.53920.8719
30.11460.10570.14980.40.61650.93530.1693-0.0558-0.21470.25040.2349-0.27130.3570.20210.14510.36620.1194-0.11510.2760.00650.3866-6.9375-2.21920.6227
40.11150.1070.25680.51720.06910.5691-0.02330.0944-0.4281-0.38450.2025-0.30380.16630.53730.04650.22720.07080.00960.4165-0.14530.3883-2.8286.0257-9.7309
50.02090.0018-0.00170.04740.06210.11080.14210.0505-0.6063-0.0251-0.06360.32130.2862-0.22670.00030.2403-0.0235-0.03260.2732-0.01720.334-21.28071.1099-8.5589
60.01820.0140.02850.0060.01860.0304-0.10950.33910.0871-0.0139-0.0262-0.0048-0.0469-0.30130.00020.32730.0241-0.06650.3703-0.01010.2804-28.286613.2003-16.2276
71.69890.84671.3551.16610.41121.52510.0974-0.0084-0.2553-0.11010.1506-0.2440.21480.2424-0.13150.07810.0412-0.01880.3599-0.12420.2647-6.69318.5494-7.426
80.08630.0728-0.07420.0606-0.05780.0589-0.03470.28430.0548-0.14980.1145-0.1735-0.13550.4370.00090.2124-0.0405-0.00680.2934-0.01140.1943-8.787621.1045-10.7187
90.20470.25790.05730.3120.08060.02630.06970.008-0.14810.10360.105-0.0977-0.11720.04230.00010.16290.0128-0.0370.23820.00010.1973-13.300910.1977-1.2299
100.07670.0801-0.02230.17260.07890.0879-0.0488-0.14210.14790.0936-0.0065-0.0599-0.32530.1184-0.00220.20990.0398-0.02470.2586-0.04990.1814-12.576722.33852.396
110.25320.043-0.03260.25980.07350.0955-0.0475-0.57160.11160.250.13990.0079-0.0976-0.1284-0.06260.24730.07-0.01540.3118-0.04580.2437-15.30116.78784.4651
120.0420.03150.01290.07850.00760.0009-0.0522-0.15470.0803-0.10060.12320.2064-0.0714-0.21560.0010.17240.0358-0.0150.2324-0.00940.1767-19.045418.7072-8.0929
130.14820.07940.18540.12120.08780.2410.128-0.0493-0.1419-0.0710.02520.1046-0.11830.11340.03960.1668-0.0118-0.01560.2744-0.05710.2218-7.216220.1802-0.0134
140.84750.12950.38841.2551-0.18690.58550.0607-0.0043-0.0824-0.16770.2856-0.32730.14720.03670.12550.11240.0371-0.03050.2856-0.08290.2274-12.49259.6643-8.4581
150.1871-0.1610.17390.1433-0.15610.1873-0.1781-0.15750.1134-0.37140.2319-0.1772-0.0339-0.28640.00520.3992-0.10440.02950.3596-0.02070.244-15.217716.4338-26.1929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 188:204)A188 - 204
2X-RAY DIFFRACTION2(chain A and resid 205:215)A205 - 215
3X-RAY DIFFRACTION3(chain A and resid 216:232)A216 - 232
4X-RAY DIFFRACTION4(chain A and resid 233:266)A233 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:283)A267 - 283
6X-RAY DIFFRACTION6(chain A and resid 284:293)A284 - 293
7X-RAY DIFFRACTION7(chain A and resid 294:306)A294 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:320)A307 - 320
9X-RAY DIFFRACTION9(chain A and resid 321:335)A321 - 335
10X-RAY DIFFRACTION10(chain A and resid 336:350)A336 - 350
11X-RAY DIFFRACTION11(chain A and resid 351:361)A351 - 361
12X-RAY DIFFRACTION12(chain A and resid 362:371)A362 - 371
13X-RAY DIFFRACTION13(chain A and resid 372:381)A372 - 381
14X-RAY DIFFRACTION14(chain A and resid 382:392)A382 - 392
15X-RAY DIFFRACTION15(chain A and resid 393:403)A393 - 403

+
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