[English] 日本語
Yorodumi
- PDB-3ior: Huntingtin amino-terminal region with 17 Gln residues - crystal C95 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ior
TitleHuntingtin amino-terminal region with 17 Gln residues - crystal C95
ComponentsMaltose-binding protein, huntingtin fusion protein
KeywordsSIGNALING PROTEIN / Huntingtin / Htt-Ex1 / HD / Sugar transport / Transport / Apoptosis / Disease mutation / Nucleus / Phosphoprotein
Function / homology
Function and homology information


regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly ...regulation of cAMP-dependent protein kinase activity / regulation of phosphoprotein phosphatase activity / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / microtubule-based transport / vocal learning / regulation of CAMKK-AMPK signaling cascade / positive regulation of mitophagy / profilin binding / vesicle transport along microtubule / positive regulation of cilium assembly / presynaptic cytosol / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of aggrephagy / postsynaptic cytosol / positive regulation of lipophagy / dynein intermediate chain binding / detection of maltose stimulus / maltose transport complex / beta-tubulin binding / Golgi organization / carbohydrate transport / establishment of mitotic spindle orientation / dynactin binding / Regulation of MECP2 expression and activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / autophagosome / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / inclusion body / heat shock protein binding / centriole / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / cytoplasmic vesicle membrane / 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 / DNA damage response / dendrite / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / membrane / nucleus / 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 K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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: Database references / Structure summary
Category: pdbx_entry_details / struct_ref ...pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_entry_details.sequence_details / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose-binding protein, huntingtin fusion protein
B: Maltose-binding protein, huntingtin fusion protein
C: Maltose-binding protein, huntingtin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,58315
Polymers147,9503
Non-polymers63312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-30.5 kcal/mol
Surface area49960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.080, 100.980, 137.860
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

-
Components

#1: Protein Maltose-binding protein, huntingtin fusion protein / MMBP / Maltodextrin-binding protein / and Huntington disease protein / HD protein


Mass: 49316.715 Da / Num. of mol.: 3 / Fragment: Fusion protein, see remark 999
Source method: isolated from a genetically manipulated source
Details: Huntingtin-Ex1 / Source: (gene. exp.) Escherichia coli K-12, Homo sapiens / 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.: 6 / 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.96 %
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

-
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: 2.68→50 Å / Num. obs: 20472 / Redundancy: 2.5 % / Rsym value: 0.09

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→37.36 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.857 / SU B: 68.196 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.697 / 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
Rfree0.26723 1591 7.2 %RANDOM
Rwork0.25751 ---
obs0.2582 20472 84.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.475 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å2-1.82 Å2
2--1.76 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 3.6→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9154 0 12 0 9166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.96612749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55325.943387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.159151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9381515
X-RAY DIFFRACTIONr_chiral_restr0.0820.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217144
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_it1.1281.55994
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07629553
X-RAY DIFFRACTIONr_scbond_it2.06733382
X-RAY DIFFRACTIONr_scangle_it3.4014.53196
X-RAY DIFFRACTIONr_rigid_bond_restr1.25339376
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 73 -
Rwork0.334 940 -
obs--53.04 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more