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- PDB-4v6b: Crystal structure of human ferritin Phe167SerfsX26 mutant. -

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Basic information

Entry
Database: PDB / ID: 4v6b
TitleCrystal structure of human ferritin Phe167SerfsX26 mutant.
ComponentsFerritin
KeywordsIRON STORAGE / iron storage protein / disorder / Iron / Metal-binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsHurley, T.D. / Vidal, R.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Unraveling of the E-helices and disruption of 4-fold pores are associated with iron mishandling in a mutant ferritin causing neurodegeneration
Authors: Baraibar, M.A. / Muhoberac, B.B. / Garringer, H.J. / Hurley, T.D. / Vidal, R.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: Iron-mediated aggregation and a localized structural change characterize ferritin from a mutant light chain polypeptide that causes neurodegeneration.
Authors: Baraibar, M.A. / Barbeito, A.G. / Muhoberac, B.B. / Vidal, R.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3HX2, 3HX5, 3HX7
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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 / struct_conn / struct_ref_seq_dif
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Ferritin
Aa: Ferritin
AB: Ferritin
Ab: Ferritin
AC: Ferritin
Ac: Ferritin
AD: Ferritin
Ad: Ferritin
AE: Ferritin
Ae: Ferritin
AF: Ferritin
Af: Ferritin
AG: Ferritin
Ag: Ferritin
AH: Ferritin
Ah: Ferritin
AI: Ferritin
Ai: Ferritin
AJ: Ferritin
Aj: Ferritin
AK: Ferritin
Ak: Ferritin
AL: Ferritin
Al: Ferritin
AM: Ferritin
Am: Ferritin
AN: Ferritin
An: Ferritin
AO: Ferritin
Ao: Ferritin
AP: Ferritin
Ap: Ferritin
AQ: Ferritin
Aq: Ferritin
AR: Ferritin
Ar: Ferritin
AS: Ferritin
As: Ferritin
AT: Ferritin
At: Ferritin
AU: Ferritin
Au: Ferritin
AV: Ferritin
Av: Ferritin
AW: Ferritin
Aw: Ferritin
AX: Ferritin
Ax: Ferritin
BA: Ferritin
Ba: Ferritin
BB: Ferritin
Bb: Ferritin
BC: Ferritin
Bc: Ferritin
BD: Ferritin
Bd: Ferritin
BE: Ferritin
Be: Ferritin
BF: Ferritin
Bf: Ferritin
BG: Ferritin
Bg: Ferritin
BH: Ferritin
Bh: Ferritin
BI: Ferritin
Bi: Ferritin
BJ: Ferritin
Bj: Ferritin
BK: Ferritin
Bk: Ferritin
BL: Ferritin
Bl: Ferritin
BM: Ferritin
Bm: Ferritin
BN: Ferritin
Bn: Ferritin
BO: Ferritin
Bo: Ferritin
BP: Ferritin
Bp: Ferritin
BQ: Ferritin
Bq: Ferritin
BR: Ferritin
Br: Ferritin
BS: Ferritin
Bs: Ferritin
BT: Ferritin
Bt: Ferritin
BU: Ferritin
Bu: Ferritin
BV: Ferritin
Bv: Ferritin
BW: Ferritin
Bw: Ferritin
BX: Ferritin
Bx: Ferritin
CA: Ferritin
Ca: Ferritin
CB: Ferritin
Cb: Ferritin
CC: Ferritin
Cc: Ferritin
CD: Ferritin
Cd: Ferritin
CE: Ferritin
Ce: Ferritin
CF: Ferritin
Cf: Ferritin
CG: Ferritin
Cg: Ferritin
CH: Ferritin
Ch: Ferritin
CI: Ferritin
Ci: Ferritin
CJ: Ferritin
Cj: Ferritin
CK: Ferritin
Ck: Ferritin
CL: Ferritin
Cl: Ferritin
CM: Ferritin
Cm: Ferritin
CN: Ferritin
Cn: Ferritin
CO: Ferritin
Co: Ferritin
CP: Ferritin
Cp: Ferritin
CQ: Ferritin
Cq: Ferritin
CR: Ferritin
Cr: Ferritin
CS: Ferritin
Cs: Ferritin
CT: Ferritin
Ct: Ferritin
CU: Ferritin
Cu: Ferritin
CV: Ferritin
Cv: Ferritin
CW: Ferritin
Cw: Ferritin
CX: Ferritin
Cx: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,095,372192
Polymers3,093,448144
Non-polymers1,92448
Water48,8572712
1
AA: Ferritin
AB: Ferritin
AC: Ferritin
AD: Ferritin
AE: Ferritin
AF: Ferritin
AG: Ferritin
AH: Ferritin
AI: Ferritin
AJ: Ferritin
AK: Ferritin
AL: Ferritin
AM: Ferritin
AN: Ferritin
AO: Ferritin
AP: Ferritin
AQ: Ferritin
AR: Ferritin
AS: Ferritin
AT: Ferritin
AU: Ferritin
AV: Ferritin
AW: Ferritin
AX: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Aa: Ferritin
Ab: Ferritin
Ac: Ferritin
Ad: Ferritin
Ae: Ferritin
Af: Ferritin
Ag: Ferritin
Ah: Ferritin
Ai: Ferritin
Aj: Ferritin
Ak: Ferritin
Al: Ferritin
Am: Ferritin
An: Ferritin
Ao: Ferritin
Ap: Ferritin
Aq: Ferritin
Ar: Ferritin
As: Ferritin
At: Ferritin
Au: Ferritin
Av: Ferritin
Aw: Ferritin
Ax: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
BA: Ferritin
BB: Ferritin
BC: Ferritin
BD: Ferritin
BE: Ferritin
BF: Ferritin
BG: Ferritin
BH: Ferritin
BI: Ferritin
BJ: Ferritin
BK: Ferritin
BL: Ferritin
BM: Ferritin
BN: Ferritin
BO: Ferritin
BP: Ferritin
BQ: Ferritin
BR: Ferritin
BS: Ferritin
BT: Ferritin
BU: Ferritin
BV: Ferritin
BW: Ferritin
BX: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Ba: Ferritin
Bb: Ferritin
Bc: Ferritin
Bd: Ferritin
Be: Ferritin
Bf: Ferritin
Bg: Ferritin
Bh: Ferritin
Bi: Ferritin
Bj: Ferritin
Bk: Ferritin
Bl: Ferritin
Bm: Ferritin
Bn: Ferritin
Bo: Ferritin
Bp: Ferritin
Bq: Ferritin
Br: Ferritin
Bs: Ferritin
Bt: Ferritin
Bu: Ferritin
Bv: Ferritin
Bw: Ferritin
Bx: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
CA: Ferritin
CB: Ferritin
CC: Ferritin
CD: Ferritin
CE: Ferritin
CF: Ferritin
CG: Ferritin
CH: Ferritin
CI: Ferritin
CJ: Ferritin
CK: Ferritin
CL: Ferritin
CM: Ferritin
CN: Ferritin
CO: Ferritin
CP: Ferritin
CQ: Ferritin
CR: Ferritin
CS: Ferritin
CT: Ferritin
CU: Ferritin
CV: Ferritin
CW: Ferritin
CX: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
Ca: Ferritin
Cb: Ferritin
Cc: Ferritin
Cd: Ferritin
Ce: Ferritin
Cf: Ferritin
Cg: Ferritin
Ch: Ferritin
Ci: Ferritin
Cj: Ferritin
Ck: Ferritin
Cl: Ferritin
Cm: Ferritin
Cn: Ferritin
Co: Ferritin
Cp: Ferritin
Cq: Ferritin
Cr: Ferritin
Cs: Ferritin
Ct: Ferritin
Cu: Ferritin
Cv: Ferritin
Cw: Ferritin
Cx: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,89532
Polymers515,57524
Non-polymers3218
Water41423
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.340, 236.940, 249.710
Angle α, β, γ (deg.)94.69, 115.06, 114.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Ferritin


Mass: 21482.279 Da / Num. of mol.: 144 / Mutation: Phe167SerfsX26
Source method: isolated from a genetically manipulated source
Details: The His-tag was cleaved from the purified protein using Factor Xa, leaving an additional Arg residue N-terminal to the initiator methionine.
Source: (gene. exp.) Homo sapiens (human) / Gene: FTL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6S4P3
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2712 / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Description: The three coordinate split files (3HX2, 3HX5, 3HX7) comprise the complete asymmetric unit composed of six chains and described in remark 400. The structure factor file deposited with ...Description: The three coordinate split files (3HX2, 3HX5, 3HX7) comprise the complete asymmetric unit composed of six chains and described in remark 400. The structure factor file deposited with each of the three split files is identical and is complete in each file.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH 6.5, 5% w/v PEG 6000, 2% v/v Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 846572 / % possible obs: 94.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Χ2: 1.036 / Net I/σ(I): 9.653
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.91 / Num. unique all: 56467 / Χ2: 0.934 / % possible all: 62.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.473 / Cor.coef. Fo:Fc: 0.513 / Cor.coef. Io to Ic: 0.501
Highest resolutionLowest resolution
Rotation5.5 Å35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FG8

2fg8


Resolution: 2.85→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.764 / Isotropic thermal model: Restrained isotropic / Cross valid method: refinement / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 42235 4.8 %Random
Rwork0.249 ---
obs-844042 95.4 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso max: 128.65 Å2 / Biso mean: 54.76 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--4.036 Å2-11.87 Å2-7.302 Å2
2---4.121 Å21.519 Å2
3---8.157 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms61936 0 16 1282 63234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7862
X-RAY DIFFRACTIONc_scbond_it2.4642.5
X-RAY DIFFRACTIONc_mcangle_it2.9392.5
X-RAY DIFFRACTIONc_scangle_it3.9843
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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