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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jgp
TitleCrystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate at 318K
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 / 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 / cytoplasm / cytosol
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
NICKEL (II) ION / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 6.42 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3215
Polymers21,1221
Non-polymers1994
Water00
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)511,713120
Polymers506,93524
Non-polymers4,77896
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area90700 Å2
ΔGint-281 kcal/mol
Surface area142750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.100, 154.100, 154.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-203-

NI

31A-204-

NA

-
Components

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


Mass: 21122.291 Da / Num. of mol.: 1
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM NiCl2, 12.6% PEP Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 5 mM H2fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

-
Data collection

DiffractionMean temperature: 318 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 6.42→62.91 Å / Num. obs: 1225 / % possible obs: 99.6 % / Redundancy: 17.8 % / Biso Wilson estimate: 227.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.3
Reflection shellResolution: 6.42→6.65 Å / Num. unique obs: 117 / CC1/2: 0.827

-
Processing

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

5cmq


Resolution: 6.42→62.91 Å / SU ML: 0.3354 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3017 122 10.07 %
Rwork0.2471 1090 -
obs0.2532 1212 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 337.88 Å2
Refinement stepCycle: LAST / Resolution: 6.42→62.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 4 0 1421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00091447
X-RAY DIFFRACTIONf_angle_d0.30421950
X-RAY DIFFRACTIONf_chiral_restr0.0294203
X-RAY DIFFRACTIONf_plane_restr0.0021259
X-RAY DIFFRACTIONf_dihedral_angle_d3.2796187
LS refinement shellResolution: 6.42→62.91 Å
RfactorNum. reflection% reflection
Rfree0.3017 122 -
Rwork0.2471 1090 -
obs--99.1 %
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)
11.188990664880.38115629647-1.479963349010.987243108385-0.1862349801022.007161275780.239745424865-1.51642321551.200971193561.484452224290.877970551598-0.130739219917-0.07140824561761.8905304393-0.1635247416975.176112136420.0850684676821-1.143512066042.28025223199-1.442773226123.55701406028.2474220052637.771902570635.5530777303
24.68838967774-0.72357371646-1.359532297332.33091639225-0.5025808220390.6191800072222.255904310870.4232230683290.468388059107-0.1615216431290.321907380577-1.67313876825-1.045315653591.809864689110.3068851456274.14747095649-0.1466136024730.6790477233182.66545481851-1.763418322273.745310001386.6218594773333.113997824828.6438827491
30.435344751476-0.840350097814-0.5629552902372.253381388140.497852708611.06129434318-0.273395366914-1.238852201531.614538717230.7519290087130.0664318500104-0.725928213438-1.106153205590.272604453538-0.5830413301554.1819894636-1.21811337667-0.9354328930352.68238649702-1.750615189472.9771158879814.749412067340.093451837333.8432826424
41.09093771250.6454099510210.7610486372730.3796719740480.4531034299160.534848483195-0.00315222629625-1.018553581031.228718420410.885501317116-0.30569233508-0.972651066295-0.4525910060740.137275000626-0.04491601502825.02196094104-1.115787384380.01759574612231.53677659185-1.089681253793.664759648677.8441291108845.96784757513.7098757116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 176 )

+
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