[English] 日本語
Yorodumi
- PDB-8a0g: Human deoxyhypusine synthase with trapped transition state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a0g
TitleHuman deoxyhypusine synthase with trapped transition state
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE / Hypusination / posttranslational modification
Function / homology
Function and homology information


peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
1,3-DIAMINOPROPANE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SPERMIDINE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWator, E. / Wilk, P. / Grudnik, P.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders.
Authors: Elżbieta Wątor / Piotr Wilk / Artur Biela / Michał Rawski / Krzysztof M Zak / Wieland Steinchen / Gert Bange / Sebastian Glatt / Przemysław Grudnik /
Abstract: Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The ...Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
History
DepositionMay 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1827
Polymers82,5172
Non-polymers1,6645
Water5,495305
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,36414
Polymers165,0354
Non-polymers3,32910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area32750 Å2
ΔGint-165 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.950, 106.950, 161.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41258.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: K329 is posttranslationally modified to deoxyhypusine i.e. 5GG.
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase

-
Non-polymers , 5 types, 310 molecules

#2: Chemical ChemComp-13D / 1,3-DIAMINOPROPANE


Mass: 74.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10N2
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml protein solution was mixed with equal volume of mother liquor consisting of 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix, PEG 1000, PEG 3350 and 100 mM Tris-Bicine pH 8.5.

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2021
RadiationMonochromator: CCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.84→46.52 Å / Num. obs: 93129 / % possible obs: 99.9 % / Redundancy: 9.905 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.192 / Rrim(I) all: 0.203 / Net I/σ(I): 8.58 / Num. measured all: 922420
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.9510.1011.9670.9715016614947148660.5492.07299.5
1.95-2.089.7231.1551.8913593813983139810.7771.22100
2.08-2.2510.3080.7573.1713506013102131020.9030.797100
2.25-2.479.7520.4844.8811740312042120390.9570.511100
2.47-2.7610.1350.3197.3811105610958109580.9780.336100
2.76-3.189.8540.19511.6895520969496940.990.206100
3.18-3.899.9880.10620.3382379824882480.9960.111100
3.89-5.489.4490.07228.3461198647864770.9970.076100
5.48-46.528.9530.0623033700377837640.9980.06699.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XXJ

6xxj


Resolution: 1.84→46.52 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1641 --
Rwork0.1471 --
obs0.1475 93096 99.86 %
Displacement parametersBiso max: 170.72 Å2 / Biso mean: 37.565 Å2 / Biso min: 16.71 Å2
Refinement stepCycle: LAST / Resolution: 1.84→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 111 305 5720
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)
10.01120.00690.00640.00440.00380.00390.14370.13530.15630.1553-0.0772-0.10170.04790.0305-00.8815-0.1289-0.05261.4088-0.03851.0298-15.883815.739942.0633
20.023-0.0214-0.02680.0339-0.0020.0613-0.0138-0.03440.0005-0.03080.1119-0.1536-0.29370.32150.00140.3471-0.10950.01750.2955-0.01270.3186-33.9125.537220.1709
30.3417-0.18860.01930.3359-0.07420.0662-0.08290.1927-0.0328-0.22460.0928-0.221-0.01360.1444-0.1220.3022-0.13270.08210.3525-0.04760.2821-27.969610.02583.6799
40.42250.11090.04850.75150.05220.9478-0.0530.07060.0132-0.18870.08040.01390.02050.0397-00.2751-0.05970.00830.2316-0.00330.2256-46.4533-3.3492-0.1107
50.0067-0.0439-0.02350.2130.13810.194-0.0575-0.02580.0905-0.07140.1004-0.2557-0.04120.24590.00710.2391-0.05060.03690.2947-0.01890.3071-32.13964.738812.7216
69.50257.1219-4.81062-9.35566.72790.04491.8690.2860.2386-0.2667-0.0420.1468-0.75410.19870.9156-0.0153-0.09130.9487-0.07680.9416-36.05518.6704-9.3289
70.0213-0.00650.00840.0387-0.04060.0434-0.0006-0.0597-0.1110.28350.00730.13540.2222-0.0944-0.00010.35760.04410.00710.25550.02310.3015-49.7366-18.139846.4851
80.4457-0.1831-0.06530.30280.00620.15750.01880.0699-0.019-0.01040.02180.13670.2563-0.23630.04190.3282-0.0776-0.03260.22780.02670.2556-58.2756-27.523721.7163
90.49960.0390.01320.5737-0.13041.0809-0.02130.0216-0.0282-0.11930.0744-0.04110.24430.10.00050.25320.0270.01060.168-0.02570.2047-40.5111-20.958113.9032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 27 )B9 - 27
2X-RAY DIFFRACTION2chain 'B' and (resid 28 through 53 )B28 - 53
3X-RAY DIFFRACTION3chain 'B' and (resid 54 through 97 )B54 - 97
4X-RAY DIFFRACTION4chain 'B' and (resid 98 through 307 )B98 - 307
5X-RAY DIFFRACTION5chain 'B' and (resid 308 through 362 )B308 - 362
6X-RAY DIFFRACTION6chain 'B' and (resid 363 through 363 )B363
7X-RAY DIFFRACTION7chain 'A' and (resid 28 through 53 )A28 - 53
8X-RAY DIFFRACTION8chain 'A' and (resid 54 through 97 )A54 - 97
9X-RAY DIFFRACTION9chain 'A' and (resid 98 through 363 )A98 - 363

+
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