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- PDB-5up7: Crystal Structure of the Ni-bound Human Heavy-Chain Ferritin 122H... -

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Basic information

Entry
Database: PDB / ID: 5up7
TitleCrystal Structure of the Ni-bound Human Heavy-Chain Ferritin 122H-delta C-star variant
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Node / Maxi-ferritin
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / 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
NICKEL (II) ION / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBailey, J.B. / Zhang, L. / Chiong, J.A. / Ahn, S. / Tezcan, F.A.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Synthetic Modularity of Protein-Metal-Organic Frameworks.
Authors: Bailey, J.B. / Zhang, L. / Chiong, J.A. / Ahn, S. / Tezcan, F.A.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Database references / Category: citation / diffrn_detector
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_detector.detector
Revision 1.2Oct 4, 2023Group: 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 / refine / refine_hist / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,59310
Polymers21,1221
Non-polymers4719
Water5,891327
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)518,242240
Polymers506,93524
Non-polymers11,307216
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_775-y+2,-x+2,-z1
crystal symmetry operation15_575y,-x+2,z1
crystal symmetry operation16_755-y+2,x,z1
crystal symmetry operation17_566x,z+1,-y+11
crystal symmetry operation18_764-x+2,z+1,y-11
crystal symmetry operation19_766-x+2,-z+1,-y+11
crystal symmetry operation20_564x,-z+1,y-11
crystal symmetry operation21_656z+1,y,-x+11
crystal symmetry operation22_674z+1,-y+2,x-11
crystal symmetry operation23_654-z+1,y,x-11
crystal symmetry operation24_676-z+1,-y+2,-x+11
Buried area99810 Å2
ΔGint-461 kcal/mol
Surface area135800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.150, 180.150, 180.150
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-203-

NI

21A-204-

NI

31A-206-

CA

41A-207-

CA

51A-208-

CL

61A-324-

HOH

71A-484-

HOH

81A-509-

HOH

91A-543-

HOH

101A-546-

HOH

111A-567-

HOH

121A-577-

HOH

131A-601-

HOH

141A-611-

HOH

151A-615-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 336 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir: 500 uL total volume: 25 mM Tris (pH 8), 10 mM CaCl2, 1 mM NiCl2, 1% PEG 6000 Sitting Drop: 2 uL reservoir, 2 uL of 12.5 uM ferritin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→52.005 Å / Num. obs: 24176 / % possible obs: 100 % / Redundancy: 10.3 % / Net I/σ(I): 12.5
Reflection shellHighest resolution: 1.79 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMR

5cmr


Resolution: 1.79→52.005 Å / Cross valid method: THROUGHOUT / σ(I): 1.34
RfactorNum. reflection
Rwork0.159 -
obs0.1606 24144
Rfree-1215
Refinement stepCycle: LAST / Resolution: 1.79→52.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 12 327 1744
LS refinement shellResolution: 1.79→1.8618 Å
RfactorNum. reflection% reflection
Rfree0.2787 121 -
Rwork0.2132 2490 -
obs--100 %

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