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- PDB-1z6o: Crystal Structure of Trichoplusia ni secreted ferritin -

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Basic information

Entry
Database: PDB / ID: 1z6o
TitleCrystal Structure of Trichoplusia ni secreted ferritin
Components
  • Ferritin heavy chain
  • Ferritin light chain
KeywordsMETAL BINDING PROTEIN / Iron storage
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
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 / Ferritin
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsHamburger, A.E. / West Jr., A.P. / Hamburger, Z.A. / Hamburger, P. / Bjorkman, P.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a secreted insect ferritin reveals a symmetrical arrangement of heavy and light chains.
Authors: Hamburger, A.E. / West, A.P. / Hamburger, Z.A. / Hamburger, P. / Bjorkman, P.J.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 212 A 1 .. 212 0.000 M 1 M 1 .. 191 M 1 .. 191 0.000 M 2 A 1 .. 212 B 1 .. 212 0.000 M 2 M 1 .. 191 N 1 .. 191 0.000 M 3 A 1 .. 212 C 1 .. 212 0.000 M 3 M 1 .. 191 O 1 .. 191 0.000 M 4 A 1 .. 212 D 1 .. 212 0.000 M 4 M 1 .. 191 P 1 .. 191 0.000 M 5 A 1 .. 212 E 1 .. 212 0.000 M 5 M 1 .. 191 Q 1 .. 191 0.000 M 6 A 1 .. 212 F 1 .. 212 0.000 M 6 M 1 .. 191 R 1 .. 191 0.000 M 7 A 1 .. 212 G 1 .. 212 0.000 M 7 M 1 .. 191 S 1 .. 191 0.000 M 8 A 1 .. 212 H 1 .. 212 0.000 M 8 M 1 .. 191 T 1 .. 191 0.000 M 9 A 1 .. 212 I 1 .. 212 0.000 M 9 M 1 .. 191 U 1 .. 191 0.000 M 10 A 1 .. 212 J 1 .. 212 0.000 M 10 M 1 .. 191 V 1 .. 191 0.000 M 11 A 1 .. 212 K 1 .. 212 0.000 M 11 M 1 .. 191 W 1 .. 191 0.000 M 12 A 1 .. 212 L 1 .. 212 0.000 M 12 M 1 .. 191 X 1 .. 191 0.000 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK:NULL
Remark 999SEQUENCE GENBANK ENTRIES AAX94728 AND AAX94729 ARE PARTIAL SEQUENCES. THE HEAVY AND LIGHTCHAIN ...SEQUENCE GENBANK ENTRIES AAX94728 AND AAX94729 ARE PARTIAL SEQUENCES. THE HEAVY AND LIGHTCHAIN SEQUENCES IN THIS ENTRY ARE THE COMPLETE AND NATIVE PROCESSED FORMS OF THESE PROTEINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
B: Ferritin light chain
C: Ferritin light chain
D: Ferritin light chain
E: Ferritin light chain
F: Ferritin light chain
G: Ferritin light chain
H: Ferritin light chain
I: Ferritin light chain
J: Ferritin light chain
K: Ferritin light chain
L: Ferritin light chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,91648
Polymers553,70224
Non-polymers1,21424
Water80,2754456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130110 Å2
ΔGint-909 kcal/mol
Surface area160850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.880, 145.697, 209.158
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-153-

HIS

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.176741, -0.363143, 0.914817), (0.972285, -0.208942, 0.104903), (0.153049, 0.908003, 0.390007)15.6924, -57.7021, 23.9069
3given(-0.191461, 0.97031, 0.147787), (-0.362713, -0.209862, 0.907963), (0.912021, 0.120235, 0.392125)55.745, -27.9853, -16.9173
4given(-0.685453, 0.72807, -0.00826), (0.727997, 0.68509, -0.025914), (-0.013208, -0.023776, -0.99963)91.0261, -38.0412, 106.2082
5given(0.830859, 0.091182, -0.548962), (0.531153, -0.424177, 0.733451), (-0.165979, -0.900977, -0.400863)37.9448, -66.6422, 83.3951
6given(-0.143992, -0.817556, 0.557555), (-0.404639, 0.562815, 0.720768), (-0.903069, -0.121824, -0.411856)32.7702, -16.2741, 123.2613
7given(-0.649747, -0.162739, -0.742526), (-0.161767, -0.924837, 0.34425), (-0.742738, 0.343792, 0.574584)128.1506, -8.9298, 62.5147
8given(0.33223, -0.566315, 0.754261), (-0.565136, -0.759766, -0.321523), (0.755145, -0.319441, -0.572462)-3.6133, 48.0508, 42.5979
9given(-0.147623, -0.407349, -0.901263), (-0.820149, 0.559714, -0.11864), (0.552777, 0.721656, -0.416713)109.7063, 50.218, 44.7174
10given(-0.500125, 0.680981, 0.534921), (-0.680252, 0.07329, -0.729305), (-0.535847, -0.728624, 0.426585)52.3553, 75.3636, 59.4931
11given(-0.499594, -0.68029, -0.536295), (0.680746, 0.074542, -0.728716), (0.535715, -0.729143, 0.425864)109.5142, 1.9142, 1.7704
12given(0.832476, 0.526805, -0.171642), (0.087564, -0.430988, -0.898099), (-0.547099, 0.732616, -0.404916)17.794, 43.0515, 103.3237
Detailsthe asymmetric unit contains one biological assembly composed of 12 heavy and 12 light chains.

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Components

#1: Protein
Ferritin light chain /


Mass: 24341.078 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / Cell line: BTI-Tn-5B1-4 / References: UniProt: Q52SA8
#2: Protein
Ferritin heavy chain /


Mass: 21800.779 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) / Cell line: BTI-Tn-5B1-4 / References: UniProt: Q52SA9
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4456 / 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: 2.84 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / pH: 8
Details: 20 mM Tris, 150 mM NaCl, 0.05% sodium azide, pH 8, spontaneous in storage buffer, temperature 277K, pH 8.00

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.91→29.85 Å / Num. obs: 463420 / % possible obs: 97 % / Redundancy: 1.89 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
SCALEPACKdata scaling
PDB_EXTRACT1.401data extraction
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MFR

1mfr


Resolution: 1.91→19.98 Å / Rfactor Rfree error: 0.001 / Occupancy max: 1 / Occupancy min: 0.26 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
Details: STRICT NCS WAS USED, REFINEMENT WITH NCS CONSTRAINTS WAS PERFORMED USING CHAINS A AND M. THREE IONS(FE3 A 301, CA 5302, CA 5303) AND SIX WATER MOLECULES (HOH 1 TO HOH 6) ARE LOCATED AT ...Details: STRICT NCS WAS USED, REFINEMENT WITH NCS CONSTRAINTS WAS PERFORMED USING CHAINS A AND M. THREE IONS(FE3 A 301, CA 5302, CA 5303) AND SIX WATER MOLECULES (HOH 1 TO HOH 6) ARE LOCATED AT SPECIAL POSITIONS WITH RESPECT TO THE NCS OPERATORS. DURING REFINEMENT THE OCCUPANCIES OF THESE ATOMS WERE 0.26, 0.33, 0.33, 0.33, 0.33, 0.33, 0.33, 0.5, AND 0.5, RESPECTIVELY. IN THIS ENTRY THE OCCUPANCIES OF THESE ATOMS, AND NCS-RELATED ATOMS, ARE TWO OR THREE TIMES HIGHER REFLECTING THE EFFECT OF THE NCS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 23175 5 %THIN SHELL METHOD
Rwork0.189 ---
obs0.189 463278 96.5 %-
all-479863 --
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 49.6 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å20 Å2-1.97 Å2
2---0.51 Å20 Å2
3----4.52 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.91→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 4 375 3604
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.031.5
X-RAY DIFFRACTIONc_mcangle_it4.242
X-RAY DIFFRACTIONc_scbond_it6.342
X-RAY DIFFRACTIONc_scangle_it9.322.5
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 1.91→1.97 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 1854 4.1 %
Rwork0.265 43184 -
obs--93.7 %

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