[English] 日本語
Yorodumi
- PDB-9jiu: Ferritin mutant R63MeHis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jiu
TitleFerritin mutant R63MeHis
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / 3-methyl-histidine / apo-form / human heavy chain ferritin
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsTsou, J.-C. / Huang, K.-F. / Ko, T.-P. / Wang, Y.-S.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 107-2113-M-001-025-MY3 Taiwan
National Science Council (NSC, Taiwan)112-2113-M-001-015- Taiwan
National Science Council (NSC, Taiwan)113-2113-M-001-006- Taiwan
CitationJournal: J Am Chem Soc / Year: 2024
Title: Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme.
Authors: Jo-Chu Tsou / Chun-Ju Tsou / Chun-Hsiung Wang / An-Li A Ko / Yi-Hui Wang / Huan-Hsuan Liang / Jia-Cheng Sun / Kai-Fa Huang / Tzu-Ping Ko / Shu-Yu Lin / Yane-Shih Wang /
Abstract: Histidine modifications of proteins are broadly based on chemical methods triggering N-substitution reactions such as aza-Michael addition at histidine's moderately nucleophilic imidazole side chain. ...Histidine modifications of proteins are broadly based on chemical methods triggering N-substitution reactions such as aza-Michael addition at histidine's moderately nucleophilic imidazole side chain. While recent studies have demonstrated chemoselective, histidine-specific modifications by further exploiting imidazole's electrophilic reactivity to overcome interference from the more nucleophilic lysine and cysteine, achieving site-specific histidine modifications remains a major challenge due to the absence of spatial control over chemical processes. Herein, through X-ray crystallography and cryo-electron microscopy structural studies, we describe the rational design of a nature-inspired, noncanonical amino-acid-incorporated, human ferritin-based metalloenzyme that is capable of introducing site-specific post-translational modifications (PTMs) to histidine in peptides and proteins. Specifically, chemoenzymatic aza-Michael additions on single histidine residues were carried out on eight protein substrates ranging from 10 to 607 amino acids including the insulin peptide hormone. By introducing an insulin-targeting peptide into our metalloenzyme, we further directed modifications to be carried out site-specifically on insulin's B-chain histidine 5. The success of this biocatalysis platform outlines a novel approach in introducing residue- and, moreover, site-specific post-translational modifications to peptides and proteins, which may further enable reactions to be carried out .
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,24037
Polymers267,84912
Non-polymers2,39025
Water36,0842003
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,47974
Polymers535,69924
Non-polymers4,78050
Water43224
TypeNameSymmetry operationNumber
point symmetry operation1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.169, 219.169, 147.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11E-339-

HOH

21E-445-

HOH

31E-462-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1(chain "E" and (resid 4 through 176 or resid 200))
d_6ens_1(chain "F" and (resid 4 through 176 or resid 200))
d_7ens_1(chain "G" and (resid 4 through 176 or resid 200))
d_8ens_1(chain "H" and (resid 4 through 176 or resid 200))
d_9ens_1(chain "I" and (resid 4 through 176 or resid 200))
d_10ens_1(chain "J" and (resid 4 through 176 or resid 200))
d_11ens_1(chain "K" and (resid 4 through 176 or resid 200))
d_12ens_1(chain "L" and (resid 4 through 176 or resid 200))

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 4 - 176 / Label seq-ID: 5 - 177

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LL

NCS oper:
IDCodeMatrixVector
1given(0.00330615228707, 0.999992876238, -0.00182121661181), (-0.999994477997, 0.00330675973283, 0.000330628311549), (0.000336648281988, 0.0018201134475, 0.999998286926)0.132840642715, 114.332590927, -0.136036897915
2given(-0.00314356944262, -0.99999203527, -0.00245913957668), (0.999989974132, -0.00315138618234, 0.00318125773002), (-0.00318898209064, -0.00244911441709, 0.999991916083)114.709086154, -0.162671286814, 0.292523565537
3given(-0.999981655656, 0.00466172760369, -0.00386738250927), (-0.00466908466243, -0.999987303297, 0.00189549288035), (-0.00385849713478, 0.00191351524513, 0.999990725187)114.605200448, 114.44380712, 0.0829405934391
4given(-0.501749485671, -0.498979884, -0.706587948519), (0.50110018199, 0.498161764976, -0.707625228158), (0.705085853807, -0.70912194387, 8.65013240883E-5)166.744797363, 52.2953467985, 74.0684411111
5given(0.501217254221, 0.500983119821, 0.705547431238), (0.498169373409, 0.499625028638, -0.70866219467), (-0.707536952723, 0.706675841113, 0.000846238104145)-52.2867111596, 52.3842802004, 73.9669936331
6given(-0.50058154651, -0.502811689773, -0.704697466947), (-0.500100348643, -0.496494400522, 0.70950190383), (-0.706624197563, 0.707583009179, -0.0029203665106)166.781324997, 62.0331881686, 74.2171198699
7given(0.500729484625, 0.503189254929, 0.704322764754), (-0.497566575724, -0.498496373834, 0.709879474274), (0.708306067989, -0.705905049562, 0.000758322158925)-52.3060214694, 62.0011940461, 73.6710662796
8given(-0.498137680334, 0.501965122089, 0.707028901557), (0.50238583905, -0.497511074172, 0.707171266243), (0.706730019281, 0.707469962106, -0.00435115660578)4.97049617181, 4.68091865428, -6.89419384088
9given(-0.501373663003, 0.49898707971, -0.706849591023), (-0.495445744925, 0.504183307367, 0.707342001021), (0.709336284059, 0.704848272222, -0.0055632062246)109.705699979, 4.68773541779, -6.73862913869
10given(0.497928197379, -0.502588124737, 0.706733816319), (0.497581390059, -0.501881937153, -0.707479527213), (0.710267745658, 0.703931600393, 0.000177329469597)5.15679598064, 109.53598966, -7.13150829725
11given(0.497060946794, -0.504521313099, -0.705966472151), (-0.497506118911, 0.500879687636, -0.708242331522), (0.710927617144, 0.703262243507, -0.00203470862098)109.713234292, 109.456142802, -6.97131715813

-
Components

#1: Protein
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 22320.781 Da / Num. of mol.: 12 / Mutation: R63H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2003 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Bicine pH 8.5, 20%(v/v) PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 1, 2024
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 159010 / % possible obs: 97.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 37.41 Å2 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.08 / Rrim(I) all: 0.223 / Net I/σ(I): 8.4
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2 / Num. unique obs: 14962 / CC1/2: 0.949 / CC star: 0.987 / Rpim(I) all: 0.305 / Rrim(I) all: 0.843 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→29.89 Å / SU ML: 0.2781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.2356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 1982 1.3 %
Rwork0.2387 150838 -
obs0.2392 152820 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.14 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17080 0 118 2004 19202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003117521
X-RAY DIFFRACTIONf_angle_d0.583523574
X-RAY DIFFRACTIONf_chiral_restr0.03972468
X-RAY DIFFRACTIONf_plane_restr0.00383100
X-RAY DIFFRACTIONf_dihedral_angle_d12.94316563
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.433995144769
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.431876930565
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.400250417692
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.405303324171
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.477420698192
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.339041253189
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.43501202208
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.426176141562
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.466407144859
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.469116044628
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.41036919446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.330.35411300.30239916X-RAY DIFFRACTION87.1
2.33-2.40.32711380.280910432X-RAY DIFFRACTION91.75
2.4-2.470.36451380.286310573X-RAY DIFFRACTION92.51
2.47-2.550.32671410.27810719X-RAY DIFFRACTION93.99
2.55-2.640.31791430.27310911X-RAY DIFFRACTION95.62
2.64-2.740.30411440.259511005X-RAY DIFFRACTION96.3
2.74-2.870.31251430.252210959X-RAY DIFFRACTION95.91
2.87-3.020.29641410.250810889X-RAY DIFFRACTION95.03
3.02-3.210.30051430.245910798X-RAY DIFFRACTION94.05
3.21-3.460.29581410.241410787X-RAY DIFFRACTION93.77
3.46-3.80.24431430.213910785X-RAY DIFFRACTION93.43
3.8-4.350.23761400.211210672X-RAY DIFFRACTION91.95
4.35-5.480.20961460.206311052X-RAY DIFFRACTION94.48
5.48-29.890.25661510.245611340X-RAY DIFFRACTION93.93

+
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