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- PDB-3io4: Huntingtin amino-terminal region with 17 Gln residues - Crystal C90 -

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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


: / 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 / Golgi organization / dynein intermediate chain binding / 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 / autophagosome / cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / protein destabilization / kinase binding / p53 binding / late endosome / outer membrane-bounded periplasmic space / transmembrane transporter binding / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / protein-containing complex / nucleoplasm / identical protein binding / 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 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

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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 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
Water00
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

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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.

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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: 3.96 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

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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

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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

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