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- PDB-3alr: Crystal structure of Nanos -

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Basic information

Entry
Database: PDB / ID: 3alr
TitleCrystal structure of Nanos
ComponentsNanos protein
KeywordsMETAL BINDING PROTEIN / zinc-finger / translational repression / RNA / 3'-UTR
Function / homology
Function and homology information


female germ-line stem cell population maintenance / oocyte growth / female gamete generation / P granule / oogenesis / negative regulation of translation / mRNA binding / perinuclear region of cytoplasm / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Nanos, RNA-binding domain / Nanos/Xcat2 / Zinc finger, nanos-type / Nanos domain superfamily / Nanos RNA binding domain / Zinc finger nanos-type profile. / HIV-1 Nucleocapsid Protein / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHashimoto, H. / Hara, K. / Hishiki, A. / Kawaguchi, S. / Shichijo, N. / Nakamura, K. / Unzai, S. / Tamaru, Y. / Shimizu, T. / Sato, M.
CitationJournal: Embo Rep. / Year: 2010
Title: Crystal structure of zinc-finger domain of Nanos and its functional implications
Authors: Hashimoto, H. / Hara, K. / Hishiki, A. / Kawaguchi, S. / Shichijo, N. / Nakamura, K. / Unzai, S. / Tamaru, Y. / Shimizu, T. / Sato, M.
History
DepositionAug 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_seq_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanos protein
B: Nanos protein
C: Nanos protein
D: Nanos protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,29114
Polymers46,6374
Non-polymers65410
Water1,964109
1
A: Nanos protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8554
Polymers11,6591
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanos protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7903
Polymers11,6591
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nanos protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7903
Polymers11,6591
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nanos protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8554
Polymers11,6591
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.961, 100.961, 71.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Nanos protein


Mass: 11659.175 Da / Num. of mol.: 4
Fragment: C-terminal zinc-finger domain, UNP residues 59-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: nanos / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QRE8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 25, 2005 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23796 / % possible obs: 97.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.1 / % possible all: 80.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
SOLVEphasing
REFMAC5.6.0046refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.542 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20787 1219 5.1 %RANDOM
Rwork0.16313 ---
obs0.16527 22538 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.091 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å21.23 Å20 Å2
2--2.46 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 10 109 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211984
X-RAY DIFFRACTIONr_bond_other_d00.021382
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9382675
X-RAY DIFFRACTIONr_angle_other_deg2.67733315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.81422.69789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0241511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212237
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02438
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 64 -
Rwork0.223 1274 -
obs--100 %
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)
17.08951.2633.08970.24170.57561.3904-0.05720.08620.2980.0278-0.05860.06180.0593-0.05630.11580.1988-0.1163-0.01870.25780.00270.16818.7816-27.651434.9922
23.71581.20630.286.36741.04714.41580.0565-0.16860.04590.3362-0.073-0.39730.26480.19590.01650.09340.0008-0.02780.02360.02070.089724.8882-22.289548.8373
35.76113.9262-1.50444.2782-0.6541.2452-0.03780.11810.18950.10060.01950.39180.119-0.28010.01830.0974-0.00820.00290.09620.020.1406-24.9727-35.094749.5817
46.22770.133-4.53653.60890.27677.0312-0.25360.052-0.22620.06990.1167-0.29020.09220.45060.13690.0197-0.0015-0.01170.12410.00920.1514-10.3478-32.60637.5476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-91 - 153
2X-RAY DIFFRACTION2B88 - 152
3X-RAY DIFFRACTION3C87 - 153
4X-RAY DIFFRACTION4D90 - 144

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