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- PDB-3iov: Huntingtin amino-terminal region with 17 Gln residues - crystal C99 -

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Basic information

Entry
Database: PDB / ID: 3iov
TitleHuntingtin amino-terminal region with 17 Gln residues - crystal C99
ComponentsMaltose-binding periplasmic protein,Huntingtin
KeywordsSIGNALING PROTEIN / Huntingtin / Htt-Ex1 / HD / Sugar transport / Transport / Apoptosis / Disease mutation / Nucleus / Phosphoprotein
Function / homology
Function and homology information


: / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / vesicle transport along microtubule ...: / positive regulation of CAMKK-AMPK signaling cascade / microtubule-based transport / vocal learning / positive regulation of mitophagy / regulation of CAMKK-AMPK signaling cascade / profilin binding / positive regulation of cilium assembly / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / vesicle transport along microtubule / positive regulation of aggrephagy / positive regulation of lipophagy / detection of maltose stimulus / maltose transport complex / Golgi organization / dynein intermediate chain binding / carbohydrate transport / establishment of mitotic spindle orientation / dynactin binding / phosphoprotein phosphatase activity / Regulation of MECP2 expression and activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / postsynaptic cytosol / beta-tubulin binding / presynaptic cytosol / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / heat shock protein binding / inclusion body / centriole / ATP-binding cassette (ABC) transporter complex / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / cell chemotaxis / protein destabilization / kinase binding / p53 binding / late endosome / outer membrane-bounded periplasmic space / transmembrane transporter binding / periplasmic space / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / DNA damage response / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT ...Huntingtin / Huntingtin, middle-repeat / Huntingtin family / : / : / : / Huntingtin, N-terminal HEAT / Huntingtin, bridge / Huntingtin, N-terminal HEAT 1 / Huntingtin, C-terminal HEAT / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Armadillo-like helical / Armadillo-type fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Huntingtin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKim, M.W.
CitationJournal: Structure / Year: 2009
Title: Secondary structure of Huntingtin amino-terminal region.
Authors: Kim, M.W. / Chelliah, Y. / Kim, S.W. / Otwinowski, Z. / Bezprozvanny, I.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2015Group: Database references / Source and taxonomy
Revision 1.3Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / pdbx_validate_polymer_linkage / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _pdbx_entry_details.sequence_details / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_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_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: Maltose-binding periplasmic protein,Huntingtin
B: Maltose-binding periplasmic protein,Huntingtin
C: Maltose-binding periplasmic protein,Huntingtin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,62316
Polymers147,9503
Non-polymers67313
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-37.5 kcal/mol
Surface area50570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.820, 101.190, 134.820
Angle α, β, γ (deg.)90.00, 99.23, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Components

#1: Protein Maltose-binding periplasmic protein,Huntingtin / MBP / MMBP / Maltodextrin-binding protein / Huntington disease protein / HD protein


Mass: 49316.715 Da / Num. of mol.: 3
Fragment: Fusion protein, see remark 999,Fusion protein, see remark 999
Source method: isolated from a genetically manipulated source
Details: Huntingtin-Ex1
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, HTT, HD, IT15 / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: P42858
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
Sequence detailsENTITY 1 IS A FUSION PROTEIN OF E.COLI MALTOSE BINDING PROTEIN (UNIPROT P0AEX9 (MALE_ECOLI) ...ENTITY 1 IS A FUSION PROTEIN OF E.COLI MALTOSE BINDING PROTEIN (UNIPROT P0AEX9 (MALE_ECOLI) RESIDUES 27-384) TO N-TERMINAL RESIDUES 1-64 OF HUMAN HUNTINGTIN (UNIPROT P42858 (HD_HUMAN)) VIA LINKER AALAAAQTNAAA.

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 4000, 200 mM Zn acetate, 200 mM Sodium acetate, 100 mM Sodium Cacodylate pH 6.5-7.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K
PH range: 6.5-7.4

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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
Details: LN2 cooled first crystal, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution Si(111) double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 23670 / Redundancy: 2.8 % / Rsym value: 0.08

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IOR

3ior


Resolution: 3.7→38 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.851 / SU B: 88.189 / SU ML: 0.56 / Cross valid method: THROUGHOUT / ESU R Free: 0.723 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY. AUTHORS USED NCS RESTRAINTS IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.28039 1095 5 %RANDOM
Rwork0.26396 ---
obs0.26478 20629 92.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.4 Å2
2---1.1 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 3.7→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9198 0 13 0 9211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.96412793
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.00751201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75725.944392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.846151530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3161515
X-RAY DIFFRACTIONr_chiral_restr0.0630.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217174
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8051.56007
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50329571
X-RAY DIFFRACTIONr_scbond_it1.12633405
X-RAY DIFFRACTIONr_scangle_it1.994.53222
X-RAY DIFFRACTIONr_rigid_bond_restr0.6539412
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 67 -
Rwork0.343 1152 -
obs--71.83 %

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