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- PDB-6z3d: L-FerritinMSA -

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Basic information

Entry
Database: PDB / ID: 6z3d
TitleL-FerritinMSA
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin Iron storage protein
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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
ACETATE ION / Ferritin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDavidov, G. / Zarivach, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Ministry of Science and Technology Israel
CitationJournal: J Am Chem Soc / Year: 2020
Title: Folding of an Intrinsically Disordered Iron-Binding Peptide in Response to Sedimentation Revealed by Cryo-EM.
Authors: Geula Davidov / Gili Abelya / Ran Zalk / Benjamin Izbicki / Sharon Shaibi / Lior Spektor / Dayana Shagidov / Esther G Meyron-Holtz / Raz Zarivach / Gabriel A Frank /
Abstract: Biomineralization is mediated by specialized proteins that guide and control mineral sedimentation. In many cases, the active regions of these biomineralization proteins are intrinsically disordered. ...Biomineralization is mediated by specialized proteins that guide and control mineral sedimentation. In many cases, the active regions of these biomineralization proteins are intrinsically disordered. High-resolution structures of these proteins while they interact with minerals are essential for understanding biomineralization processes and the function of intrinsically disordered proteins (IDPs). Here we used the cavity of ferritin as a nanoreactor where the interaction between M6A, an intrinsically disordered iron-binding domain, and an iron oxide particle was visualized at high resolution by cryo-EM. Taking advantage of the differences in the electron-dose sensitivity of the protein and the iron oxide particles, we developed a method to determine the irregular shape of the particles found in our density maps. We found that the folding of M6A correlates with the detection of mineral particles in its vicinity. M6A interacts with the iron oxide particles through its C-terminal side, resulting in the stabilization of a helix at its N-terminal side. The stabilization of the helix at a region that is not in direct contact with the iron oxide particle demonstrates the ability of IDPs to respond to signals from their surroundings by conformational changes. These findings provide the first glimpse toward the long-suspected mechanism for biomineralization protein control over mineral microstructure, where unstructured regions of these proteins become more ordered in response to their interaction with the nascent mineral particles.
History
DepositionMay 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,52712
Polymers146,1726
Non-polymers3546
Water20,4831137
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,10748
Polymers584,69024
Non-polymers1,41724
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area97140 Å2
ΔGint-273 kcal/mol
Surface area138750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.297, 134.297, 166.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA2 - 18122 - 201
21THRTHRLYSLYSBB2 - 18122 - 201
12THRTHRLYSLYSAA2 - 18122 - 201
22THRTHRLYSLYSCC2 - 18122 - 201
13THRTHRLYSLYSAA2 - 18122 - 201
23THRTHRLYSLYSDD2 - 18122 - 201
14THRTHRLYSLYSAA2 - 18122 - 201
24THRTHRLYSLYSEE2 - 18122 - 201
15THRTHRLYSLYSAA2 - 18122 - 201
25THRTHRLYSLYSFF2 - 18122 - 201
16METMETHISHISBB1 - 18221 - 202
26METMETHISHISCC1 - 18221 - 202
17METMETHISHISBB1 - 18221 - 202
27METMETHISHISDD1 - 18221 - 202
18METMETHISHISBB1 - 18221 - 202
28METMETHISHISEE1 - 18221 - 202
19THRTHRLYSLYSBB2 - 18122 - 201
29THRTHRLYSLYSFF2 - 18122 - 201
110METMETHISHISCC1 - 18221 - 202
210METMETHISHISDD1 - 18221 - 202
111METMETHISHISCC1 - 18221 - 202
211METMETHISHISEE1 - 18221 - 202
112THRTHRLYSLYSCC2 - 18122 - 201
212THRTHRLYSLYSFF2 - 18122 - 201
113METMETHISHISDD1 - 18221 - 202
213METMETHISHISEE1 - 18221 - 202
114THRTHRLYSLYSDD2 - 18122 - 201
214THRTHRLYSLYSFF2 - 18122 - 201
115THRTHRLYSLYSEE2 - 18122 - 201
215THRTHRLYSLYSFF2 - 18122 - 201

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Ferritin /


Mass: 24362.076 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ftl1, Ftl1-ps1 / Plasmid: pET28a / Details (production host): bacterial host / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CPX4
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M sodium acetate pH 4.6 and 2 M sodium formate / PH range: 4.6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977999 Å / Relative weight: 1
ReflectionResolution: 1.7→166.85 Å / Num. obs: 166767 / % possible obs: 100 % / Redundancy: 26.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.044 / Rrim(I) all: 0.23 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7326.54.06581160.6060.8054.145100
1.7-1.7426.50.07211860.9980.0140.07499.4

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB3

1lb3


Resolution: 1.7→166.85 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.38 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 8321 5 %RANDOM
Rwork0.1551 ---
obs0.1561 158407 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.47 Å2 / Biso mean: 25.306 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 1.7→166.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 24 1137 9421
Biso mean--53.79 38.49 -
Num. residues----1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178103
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6411673
X-RAY DIFFRACTIONr_angle_other_deg1.5631.58218736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15551069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99421.458576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.025151620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6941590
X-RAY DIFFRACTIONr_chiral_restr0.0890.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021993
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A57820.06
12B57820.06
21A58020.06
22C58020.06
31A57820.06
32D57820.06
41A57950.07
42E57950.07
51A57510.07
52F57510.07
61B58330.06
62C58330.06
71B58390.05
72D58390.05
81B58430.07
82E58430.07
91B57100.07
92F57100.07
101C58820.06
102D58820.06
111C58890.07
112E58890.07
121C57380.07
122F57380.07
131D58970.06
132E58970.06
141D57300.06
142F57300.06
151E57690.07
152F57690.07
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.292 663 5 %
Rwork0.282 11506 -
obs--99.82 %
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)
10.55860.19840.48120.22630.24170.7297-0.014-0.01820.0606-0.0020.0066-0.0052-0.08790.02980.00750.0333-0.0103-0.00080.0088-0.00630.0237.344-27.24213.9855
20.67730.32010.27180.43090.21250.3264-0.00470.00250.0339-0.0183-0.00530.0201-0.0560.02230.010.0139-0.00530.00160.00670.00440.009220.8413-45.03083.3432
30.86730.154-0.30180.2489-0.04840.39330.0107-0.04260.09880.06420.00040.0252-0.0923-0.0193-0.01110.11070.01560.01150.0603-0.04610.0461-9.9094-19.496952.3673
40.77510.3508-0.3130.4354-0.1360.3350.0055-0.04330.09420.0433-0.00530.0433-0.0662-0.0374-0.00020.06380.03030.00710.0276-0.01390.0296-23.8692-24.677532.7113
50.2324-0.01160.00960.667-0.35330.404-0.0047-0.09850.02580.10920.0017-0.0165-0.0573-0.00780.0030.15630.0069-0.00720.1219-0.05370.02652.9621-36.942781.7606
60.1581-0.08790.05180.5493-0.46470.70530.0083-0.07680.04550.0706-0.0087-0.0423-0.03980.01110.00030.1246-0.0236-0.04590.1235-0.04390.043925.0901-35.455870.9444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 182
2X-RAY DIFFRACTION2B1 - 182
3X-RAY DIFFRACTION3C1 - 182
4X-RAY DIFFRACTION4D1 - 182
5X-RAY DIFFRACTION5E1 - 182
6X-RAY DIFFRACTION6F2 - 183

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