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- PDB-6b8f: Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid -

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Basic information

Entry
Database: PDB / ID: 6b8f
TitleContracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Hydrogel / Polymer
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, 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 / SYNCHROTRON / Resolution: 1.06 Å
AuthorsZhang, L. / Bailey, J.B. / Subramanian, R. / Tezcan, F.A.
CitationJournal: Nature / Year: 2018
Title: Hyperexpandable, self-healing macromolecular crystals with integrated polymer networks.
Authors: Zhang, L. / Bailey, J.B. / Subramanian, R.H. / Tezcan, F.A.
History
DepositionOct 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,63814
Polymers21,0851
Non-polymers55313
Water6,125340
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)519,307336
Polymers506,04624
Non-polymers13,261312
Water43224
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 area96970 Å2
ΔGint-977 kcal/mol
Surface area138090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.040, 180.040, 180.040
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-63-

ARG

21A-208-

CA

31A-210-

CA

41A-211-

CA

51A-212-

CA

61A-213-

CA

71A-332-

HOH

81A-535-

HOH

91A-597-

HOH

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Components

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


Mass: 21085.248 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, ...Details: Reservoir: 500 uL of 25 mM HEPES pH 7.0 with 10 mM CaCl2 Well: 2 uL of reservoir solution and 2 uL of 2.5 uM ferritin (by 24-mer) in 15 mM TRIS pH 7.4 with 150 mM NaCl After crystals formed, a crystal was harvested and soaked in a buffered solution comprised of 25 mM HEPES pH 7.0, 30 mM CaCl2, 8.6 % (w/v) sodium acrylate, 2.5 % (w/v) acrylamide, and 0.2 % (w/v) Bis-acrylamide overnight. Crystal was transferred to a solution containing 1 % APS and 1% TEMED with 4 M NaCl for 5 min. Crystal was then transferred to a clean slide and soaked in 30 uL H2O for 5 min. This solution was removed and the crystal was soaked in 1 M CaCl2 for 2 min. The crystal was removed, cryoprotected in perfluoro polyether, and frozen in liquid N2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.06→63.65 Å / Num. obs: 111189 / % possible obs: 99 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4683 / CC1/2: 0.897 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.06→45.01 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 6.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1026 5495 4.94 %
Rwork0.091 --
obs0.0916 111175 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 13 340 1759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131756
X-RAY DIFFRACTIONf_angle_d1.3172422
X-RAY DIFFRACTIONf_dihedral_angle_d18.762722
X-RAY DIFFRACTIONf_chiral_restr0.095255
X-RAY DIFFRACTIONf_plane_restr0.011331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.07210.17341600.17212929X-RAY DIFFRACTION84
1.0721-1.08470.1551550.14043176X-RAY DIFFRACTION90
1.0847-1.09790.13231670.12083372X-RAY DIFFRACTION96
1.0979-1.11180.13091890.1033430X-RAY DIFFRACTION99
1.1118-1.12640.11041980.09193499X-RAY DIFFRACTION99
1.1264-1.14190.10361930.0813470X-RAY DIFFRACTION100
1.1419-1.15820.07871860.07593491X-RAY DIFFRACTION100
1.1582-1.17550.09251710.07083518X-RAY DIFFRACTION100
1.1755-1.19380.07581800.0673529X-RAY DIFFRACTION100
1.1938-1.21340.08341740.0643556X-RAY DIFFRACTION100
1.2134-1.23430.07751840.06163488X-RAY DIFFRACTION100
1.2343-1.25680.07821760.06273544X-RAY DIFFRACTION100
1.2568-1.2810.07161870.06283534X-RAY DIFFRACTION100
1.281-1.30710.08171970.06483479X-RAY DIFFRACTION100
1.3071-1.33550.08741710.06873555X-RAY DIFFRACTION100
1.3355-1.36660.08442200.07013500X-RAY DIFFRACTION100
1.3666-1.40080.08091990.06843547X-RAY DIFFRACTION100
1.4008-1.43860.08681590.06753531X-RAY DIFFRACTION100
1.4386-1.4810.07411820.06753577X-RAY DIFFRACTION100
1.481-1.52880.07631720.06563539X-RAY DIFFRACTION100
1.5288-1.58340.08181810.06943582X-RAY DIFFRACTION100
1.5834-1.64680.0841740.07423574X-RAY DIFFRACTION100
1.6468-1.72180.09392010.08083554X-RAY DIFFRACTION100
1.7218-1.81260.1021960.08563571X-RAY DIFFRACTION100
1.8126-1.92610.10161880.0913601X-RAY DIFFRACTION100
1.9261-2.07480.09871720.08853602X-RAY DIFFRACTION100
2.0748-2.28360.08761650.09033655X-RAY DIFFRACTION100
2.2836-2.61410.10772000.09983645X-RAY DIFFRACTION100
2.6141-3.29330.12661920.11853697X-RAY DIFFRACTION100
3.2933-45.05060.13742060.12283935X-RAY DIFFRACTION100

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