[English] 日本語
Yorodumi
- PDB-7jgn: Crystal Structure of the Zn-bound Human Heavy-chain variant 122H-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jgn
TitleCrystal Structure of the Zn-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate collected at 100K
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Protein-MOF / Ferritin-MOF / Self-Assembly / 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 / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / 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
N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsBailey, J.B. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0003844 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks.
Authors: Bailey, J.B. / Tezcan, F.A.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: 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
Revision 1.2Oct 18, 2023Group: 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: 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
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
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
m: Ferritin heavy chain
n: Ferritin heavy chain
o: Ferritin heavy chain
p: Ferritin heavy chain
q: Ferritin heavy chain
r: Ferritin heavy chain
s: Ferritin heavy chain
t: Ferritin heavy chain
u: Ferritin heavy chain
v: Ferritin heavy chain
w: Ferritin heavy chain
x: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,023,918196
Polymers1,013,87048
Non-polymers10,048148
Water87,2294842
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
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,744102
Polymers506,93524
Non-polymers5,80978
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
m: Ferritin heavy chain
n: Ferritin heavy chain
o: Ferritin heavy chain
hetero molecules

g: Ferritin heavy chain
h: Ferritin heavy chain
i: Ferritin heavy chain
hetero molecules

j: Ferritin heavy chain
k: Ferritin heavy chain
l: Ferritin heavy chain
hetero molecules

p: Ferritin heavy chain
q: Ferritin heavy chain
r: Ferritin heavy chain
hetero molecules

a: Ferritin heavy chain
b: Ferritin heavy chain
c: Ferritin heavy chain
hetero molecules

d: Ferritin heavy chain
e: Ferritin heavy chain
f: Ferritin heavy chain
hetero molecules

s: Ferritin heavy chain
t: Ferritin heavy chain
u: Ferritin heavy chain
hetero molecules

v: Ferritin heavy chain
w: Ferritin heavy chain
x: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,17494
Polymers506,93524
Non-polymers4,23970
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,y+1/2,-z-11
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
crystal symmetry operation2_754-x+2,y+1/2,-z-11
Unit cell
Length a, b, c (Å)215.750, 215.460, 156.460
Angle α, β, γ (deg.)90.000, 89.952, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 21122.291 Da / Num. of mol.: 48
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 (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-V9D / N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide


Mass: 196.160 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H8N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4842 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM ZnCl2, 12.6% PEP Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 10 mM m-bdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 843866 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.68 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.95
Reflection shellResolution: 2.07→2.12 Å / Num. unique obs: 62629 / CC1/2: 0.541

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMQ

5cmq


Resolution: 2.07→37.8 Å / SU ML: 0.2538 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 84342 10 %
Rwork0.1843 758998 -
obs0.1889 843340 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.8 Å2
Refinement stepCycle: LAST / Resolution: 2.07→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68688 0 252 4842 73782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083105580
X-RAY DIFFRACTIONf_angle_d0.8978142302
X-RAY DIFFRACTIONf_chiral_restr0.04614783
X-RAY DIFFRACTIONf_plane_restr0.005218948
X-RAY DIFFRACTIONf_dihedral_angle_d5.546413690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.090.313828030.262425362X-RAY DIFFRACTION97.86
2.09-2.120.307428280.249225462X-RAY DIFFRACTION98.24
2.12-2.140.290227970.238725436X-RAY DIFFRACTION98.09
2.14-2.170.289128380.231125428X-RAY DIFFRACTION98.28
2.17-2.20.29628100.231825429X-RAY DIFFRACTION98.12
2.2-2.230.29228230.230625299X-RAY DIFFRACTION98.12
2.23-2.260.262828070.214425325X-RAY DIFFRACTION97.73
2.26-2.30.287527220.220624550X-RAY DIFFRACTION94.49
2.3-2.330.275427420.218724731X-RAY DIFFRACTION95.64
2.33-2.370.282328140.203425477X-RAY DIFFRACTION98.37
2.37-2.410.259328260.197725486X-RAY DIFFRACTION98.49
2.41-2.450.276728350.206125520X-RAY DIFFRACTION98.42
2.45-2.50.259628390.198825495X-RAY DIFFRACTION98.5
2.5-2.550.249428410.189125439X-RAY DIFFRACTION98.44
2.55-2.610.265728550.194325567X-RAY DIFFRACTION98.33
2.61-2.670.253528010.185125419X-RAY DIFFRACTION98.14
2.67-2.740.24328100.185125336X-RAY DIFFRACTION97.74
2.74-2.810.252827170.191224181X-RAY DIFFRACTION93.46
2.81-2.890.234228050.185125224X-RAY DIFFRACTION97.27
2.89-2.990.224728170.180925503X-RAY DIFFRACTION98.35
2.99-3.090.233328290.188825515X-RAY DIFFRACTION98.15
3.09-3.220.223328220.176725399X-RAY DIFFRACTION97.94
3.22-3.360.22528310.182225514X-RAY DIFFRACTION98.15
3.36-3.540.213528420.171825384X-RAY DIFFRACTION97.89
3.54-3.760.205227210.159624482X-RAY DIFFRACTION94.23
3.76-4.050.191728480.15725687X-RAY DIFFRACTION98.95
4.05-4.460.174228490.140125694X-RAY DIFFRACTION98.66
4.46-5.10.166428280.139525458X-RAY DIFFRACTION97.91
5.1-6.420.222728070.193225023X-RAY DIFFRACTION95.97
6.42-37.80.234828350.213825173X-RAY DIFFRACTION95.7

+
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