[English] 日本語
Yorodumi
- PDB-5n27: X-ray structure of human heavy chain ferritin (apo form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n27
TitleX-ray structure of human heavy chain ferritin (apo form)
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / 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, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsFerraro, G. / Merlino, A.
CitationJournal: Inorg Chem / Year: 2017
Title: Cisplatin Binding Sites in Human H-Chain Ferritin.
Authors: Ferraro, G. / Ciambellotti, S. / Messori, L. / Merlino, A.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,53215
Polymers21,1241
Non-polymers40714
Water5,855325
1
A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,759360
Polymers506,98724
Non-polymers9,772336
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Unit cell
Length a, b, c (Å)182.955, 182.955, 182.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-205-

CL

31A-207-

MG

41A-208-

MG

51A-312-

HOH

61A-558-

HOH

71A-617-

HOH

-
Components

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


Mass: 21124.459 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 BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M MgCl2, 0.1 M bicine pH 9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→105.63 Å / Num. obs: 27459 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.032 / Net I/σ(I): 18
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.627 / Rpim(I) all: 0.404 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y08

4y08


Resolution: 1.74→105.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.861 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19146 1378 5 %RANDOM
Rwork0.14603 ---
obs0.14823 26057 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.899 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.74→105.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 14 325 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191620
X-RAY DIFFRACTIONr_bond_other_d0.0020.021516
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9482203
X-RAY DIFFRACTIONr_angle_other_deg1.02433522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08125.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80415313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.855158
X-RAY DIFFRACTIONr_chiral_restr0.1160.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021932
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0591.66774
X-RAY DIFFRACTIONr_mcbond_other1.9471.656773
X-RAY DIFFRACTIONr_mcangle_it3.4132.474991
X-RAY DIFFRACTIONr_mcangle_other3.4162.475992
X-RAY DIFFRACTIONr_scbond_it2.9811.928846
X-RAY DIFFRACTIONr_scbond_other2.981.929847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4942.7861208
X-RAY DIFFRACTIONr_long_range_B_refined8.32816.2392316
X-RAY DIFFRACTIONr_long_range_B_other7.36814.412079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 108 -
Rwork0.266 1852 -
obs--98.89 %

+
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