[English] 日本語
Yorodumi
- PDB-3io4: Huntingtin amino-terminal region with 17 Gln residues - Crystal C90 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3io4
TitleHuntingtin amino-terminal region with 17 Gln residues - Crystal C90
ComponentsMaltose-binding periplasmic protein,Huntingtin fusion protein
KeywordsSIGNALING PROTEIN / Htt18Q-EX1 / HD / Huntingtin / Apoptosis / Cytoplasm / Disease mutation / Nucleus / Phosphoprotein / Polymorphism / Triplet repeat expansion / Ubl conjugation / Periplasm / Sugar transport / Transport
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 / beta-tubulin binding / Golgi organization / dynactin binding / establishment of mitotic spindle orientation / carbohydrate transmembrane transporter activity / Regulation of MECP2 expression and activity / autophagosome / inclusion body / heat shock protein binding / centriole / 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 / early endosome / positive regulation of apoptotic process / axon / dendrite / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 Å
AuthorsKim, M.W. / Chelliah, Y. / Kim, S.W. / Otwinowski, Z. / Bezprozvanny, I.
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 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 21, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.pdbx_description / _entity_name_com.name / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.1Sep 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 periplasmic protein,Huntingtin fusion protein
B: Maltose-binding periplasmic protein,Huntingtin fusion protein
C: Maltose-binding periplasmic protein,Huntingtin fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,71417
Polymers147,9503
Non-polymers76414
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-35 kcal/mol
Surface area52290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.950, 101.210, 142.050
Angle α, β, γ (deg.)90.00, 90.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

-
Components

#1: Protein Maltose-binding periplasmic protein,Huntingtin fusion protein / MBP / MMBP / Maltodextrin-binding protein / 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
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, HTT, HD, IT15 / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEY0, UniProt: P42858
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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 1-66 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: 68.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% polyethylene glycol, 200 mM Zn Acetate, 200 mM Sodium Acetate, 100 mM Sodium Cacodylate pH 6.5 to 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.55 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2006
Details: Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 30000 / Num. obs: 23000 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 30 Å2 / Rsym value: 0.02 / Net I/σ(I): 5.5

-
Processing

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

3ior


Resolution: 3.63→37.42 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 138.584 / SU ML: 0.846 / Cross valid method: THROUGHOUT / ESU R Free: 0.988 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30354 842 5 %RANDOM
Rwork0.2513 ---
obs0.25397 16075 64.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20.81 Å2
2--2.04 Å20 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 3.63→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 14 0 9331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229510
X-RAY DIFFRACTIONr_angle_refined_deg1.181.96212931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18451210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.63426.122410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.821151545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.691515
X-RAY DIFFRACTIONr_chiral_restr0.0770.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217290
X-RAY DIFFRACTIONr_mcbond_it0.311.56050
X-RAY DIFFRACTIONr_mcangle_it0.55229651
X-RAY DIFFRACTIONr_scbond_it0.85633460
X-RAY DIFFRACTIONr_scangle_it0.7364.53280
X-RAY DIFFRACTIONr_rigid_bond_restr1.06439510
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2304 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.640.5
Bmedium positional0.670.5
Cmedium positional0.610.5
Amedium thermal0.122
Bmedium thermal0.112
Cmedium thermal0.112
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)
15.56350.53820.27035.14932.60632.2936-0.12290.2476-0.1605-0.01390.43120.2763-0.09530.3061-0.30830.2137-0.0606-0.05490.11980.06680.3516-15.277-35.332915.9459
25.8150.15680.38272.9513-0.52423.16340.0598-0.1830.43690.1184-0.00710.07620.0201-0.0109-0.05270.05770.01060.00050.0853-0.06260.2971-9.5521-63.484428.8749
34.9153-2.29050.52516.4147-0.03645.90170.28190.48980.3396-0.87470.10630.0061-0.25670.0721-0.38820.2447-0.12660.07690.17870.03450.4464-6.9142-38.972611.2394
415.3915-10.179213.961114.0449-8.191712.8485-1.51421.83251.1513.41830.35820.4256-0.69261.84251.1561.59130.17360.77770.77830.17131.057-11.7423-54.543918.1296
57.8776-3.81899.403134.7602-30.727832.860.2259-0.44021.44763.0516-1.5810.0185-2.41760.24221.35510.3950.00530.05570.6826-0.29770.3386-24.6367-57.644633.633
66.15610.1376-9.61419.96364.491117.2391-0.1576-0.3562-0.1881.6596-0.78491.33391.05140.20720.94260.3225-0.1570.0640.53670.0320.8646-30.2301-64.921734.9305
75.753-0.5595-1.33573.0945-0.14057.4012-0.22540.110.1769-0.01240.1042-0.06590.39040.04640.12120.0580.0204-0.08760.0223-0.05640.2492-73.846-37.778217.6961
82.4682-0.4042-0.03334.0479-1.03941.65630.07980.04810.2467-0.428-0.1967-0.1601-0.20440.06890.11690.36660.1370.01720.40680.08690.3692-49.6377-19.056710.3134
94.97753.35550.76146.08950.73172.2289-0.07870.66670.085-0.55550.16130.02940.0709-0.6781-0.08250.17610.0786-0.11530.49840.01240.2818-76.6566-32.46469.6457
106.1818-3.97210.729426.159-10.953311.18881.16281.7812-0.8946-0.6823-1.9231-0.1249-0.80592.72440.76020.34640.0238-0.24521.2691-0.03170.351-59.3272-28.53527.6998
1133.45036.0064-8.62832.8065-4.29496.60911.0108-1.88992.19110.20280.15410.8722-0.3759-0.1528-1.1650.465-0.0648-0.25850.24380.06060.6035-45.0095-29.467122.5611
1223.2928-1.08845.37143.1439-2.74183.31151.34950.0843-0.60130.1599-0.51681.02010.2660.6421-0.83270.44790.31690.08580.56520.01240.5161-36.3266-31.942420.8262
131.9280.04491.54576.1015-0.74152.6642-0.1978-0.2436-0.16810.39040.07420.05320.20810.43550.12360.38040.10090.070.45060.09970.2894-41.7693-83.695835.9965
143.81750.4534-1.28544.1898-0.86132.72510.1989-0.3321-0.15470.1442-0.30190.14280.26550.1630.1030.3352-0.0376-0.06830.11960.03260.2627-71.5345-73.384932.3453
1513.23943.03034.68333.17481.01621.82770.2027-0.1333-1.0132-0.23840.06230.13450.44030.0491-0.26510.81990.16760.12180.10140.14650.4394-47.049-91.574433.0475
1620.44233.6806-8.00177.4616-5.00665.00650.42910.10360.5638-0.0033-0.22280.0889-0.08520.0887-0.20630.2812-0.0995-0.25970.05420.08630.4507-59.6832-79.737727.9105
1739.7394-18.96-0.17729.861-0.26350.2375-0.7501-0.12670.37690.24550.4391-0.7038-0.1469-0.21730.3110.50160.0374-0.13180.2483-0.32340.4513-61.1414-60.394535.2413
1835.654211.4389-10.644311.6439-7.65085.43721.3273-1.07441.87990.0616-0.6760.5746-0.21650.4807-0.65120.3049-0.0511-0.0180.0461-0.0580.747-63.8454-53.172330.3508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION2A112 - 259
3X-RAY DIFFRACTION3A260 - 314
4X-RAY DIFFRACTION4A315 - 334
5X-RAY DIFFRACTION5A335 - 352
6X-RAY DIFFRACTION6A353 - 370
7X-RAY DIFFRACTION7B2 - 111
8X-RAY DIFFRACTION8B112 - 259
9X-RAY DIFFRACTION9B260 - 314
10X-RAY DIFFRACTION10B315 - 334
11X-RAY DIFFRACTION11B335 - 352
12X-RAY DIFFRACTION12B353 - 370
13X-RAY DIFFRACTION13C1 - 111
14X-RAY DIFFRACTION14C112 - 259
15X-RAY DIFFRACTION15C260 - 314
16X-RAY DIFFRACTION16C315 - 334
17X-RAY DIFFRACTION17C335 - 352
18X-RAY DIFFRACTION18C353 - 370

+
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://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