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- PDB-4fe8: Crystal Structure of Htt36Q3H-EX1-X1-C1(Alpha) -

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Basic information

Entry
Database: PDB / ID: 4fe8
TitleCrystal Structure of Htt36Q3H-EX1-X1-C1(Alpha)
ComponentsMaltose-binding periplasmic protein,Huntingtin
KeywordsSIGNALING PROTEIN / alpha helix / loop / beta-strand hairpin / Beta strand hairpin / Disease protein
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 / beta-tubulin binding / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / Golgi organization / dynactin binding / establishment of mitotic spindle orientation / carbohydrate transmembrane transporter activity / Regulation of MECP2 expression and activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / autophagosome / 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 / dendrite / apoptotic process / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex / nucleoplasm / membrane / 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 (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, M.
CitationJournal: Prion / Year: 2013
Title: Beta conformation of polyglutamine track revealed by a crystal structure of Huntingtin N-terminal region with insertion of three histidine residues.
Authors: Kim, M.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_mutation / _entity_name_com.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)152,35334
Polymers150,3253
Non-polymers2,02831
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-20 kcal/mol
Surface area53310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.052, 177.278, 78.868
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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


Mass: 50108.320 Da / Num. of mol.: 3
Fragment: Huntingtin protein exon1 domain (UNP residues 1-164),Huntingtin protein exon1 domain (UNP residues 1-164)
Mutation: HQHQH,HQHQH
Source method: isolated from a genetically manipulated source
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.: 31 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIS A FUSION PROTEIN OF E.COLI MALTOSE BINDING PROTEIN (UNIPROT P0AEX9 (MALE_ECOLI) RESIDUES 27-384) ...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)

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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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG12K, Na Acetate, Zn Acetate, Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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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 315r / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. all: 75674 / Num. obs: 66012 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 85

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 33.001 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1942 5 %RANDOM
Rwork0.2267 ---
obs0.2291 38580 95.87 %-
all-40321 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60 Å2 / Biso mean: 90.867 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å22.49 Å2
2---6.3 Å20 Å2
3---4.35 Å2
Refinement stepCycle: LAST / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9447 0 31 148 9626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229680
X-RAY DIFFRACTIONr_angle_refined_deg0.8481.95413131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.85651215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71426.154442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.679151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9291516
X-RAY DIFFRACTIONr_chiral_restr0.0580.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217409
X-RAY DIFFRACTIONr_mcbond_it0.1151.56047
X-RAY DIFFRACTIONr_mcangle_it0.21729672
X-RAY DIFFRACTIONr_scbond_it0.24133633
X-RAY DIFFRACTIONr_scangle_it0.4224.53459
Refine LS restraints NCS

Ens-ID: 1 / Number: 2698 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.220.5
2BMEDIUM POSITIONAL0.240.5
3CMEDIUM POSITIONAL0.190.5
1AMEDIUM THERMAL0.082
2BMEDIUM THERMAL0.072
3CMEDIUM THERMAL0.072
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 150 -
Rwork0.335 2774 -
all-2924 -
obs--99.42 %
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)
17.12760.2571-1.85415.95839.097515.3271-0.16070.5305-0.7332-0.1280.08940.90170.5213-1.56460.07130.147-0.2199-0.06340.61270.17430.366-29.037867.9727-3.8449
23.42764.2585-1.76718.867-5.109310.56670.0354-0.1853-0.24530.88230.32050.3355-0.4726-0.5447-0.35590.2184-0.00990.00730.33050.04260.0898-19.74571.58118.3225
39.03933.8656-2.51217.5338-3.8338.98920.1776-0.07820.4813-0.0944-0.661-0.9594-0.36650.54860.48330.2858-0.04980.07340.2065-0.08590.2399-9.873477.0693-3.9099
43.41770.16652.8985.60322.42458.2086-0.1270.47750.779-1.139-0.21580.5445-1.4812-0.86760.34290.49540.1246-0.00630.46530.15010.3067-21.4418110.9937-1.588
510.5065-0.65340.70359.2734-0.7242.6096-0.2838-0.037-0.36040.39250.2953-0.56650.15850.5022-0.01150.2501-0.01410.11370.21410.00460.1615-7.220993.23039.8807
617.811-6.9701-4.862119.96075.44816.20530.4138-1.08611.2261-0.35420.03780.6144-0.7842-0.4396-0.45160.38110.03620.09640.1780.0130.2032-14.3151110.479611.683
78.429-4.6347-1.70378.79961.45575.3426-0.37550.33380.5179-0.5645-0.05281.5374-0.0581-2.08170.42830.32220.0796-0.10730.69030.0210.5014-30.1505101.93040.7052
80.80391.3527-0.376111.3251.40381.9074-0.03120.41340.0425-0.51650.08040.28110.1699-0.4314-0.04910.1585-0.06930.04620.38590.03030.0266-18.777781.2563-5.6348
95.9089-2.38063.660811.0533-0.9656-0.2827-0.1080.33310.3591-0.9970.19330.0992-0.3005-0.2668-0.08530.3267-0.06880.08130.36030.00970.0753-16.149989.5585-6.8521
100.63770.03022.103539.01735.2380.8676-0.2745-0.75090.02771.2344-0.1469-0.26880.24190.1460.42140.4137-0.09290.1040.35320.10480.0697-11.731798.031520.2644
1117.44850.32064.028510.45691.30776.0599-0.0316-1.2189-0.86111.58890.0304-0.64790.50850.02480.00130.56810.0935-0.0480.24860.22130.463418.870351.652152.4311
122.16831.4243-0.60838.44061.86216.96560.0794-0.3651-0.16370.3956-0.40960.5584-0.2655-0.39460.33030.26930.16960.04650.23230.0350.310211.440663.328944.8523
130.08840.37750.010716.58324.954610.19050.41390.04660.1307-0.6567-0.0483-1.387-0.31990.5011-0.36560.2360.24890.19270.22850.09310.530121.157257.713432.0541
147.4002-0.0872.37099.78330.78582.56330.78510.4852-2.148-0.3234-0.11980.25291.6658-0.1746-0.66530.90080.0948-0.12850.2447-0.09960.7101-4.770136.445218.9126
158.80323.9977-1.34667.6057-1.54748.25110.04180.24280.3879-0.3908-0.0849-0.0832-0.08290.2340.04310.27050.18740.10270.2020.0140.04312.671260.648321.3712
1618.529915.92748.229612.81028.35422.3071-0.1950.9679-0.2983-0.46931.39170.54160.7387-1.1986-1.19670.44270.1281-0.05630.3803-0.05160.3087-11.326449.66615.5512
1710.7438-1.93931.503-2.64950.4213.9422-0.2145-1.0996-1.9890.6640.34550.69731.1944-0.3185-0.1310.759-0.0941-0.00960.31290.20570.7353-4.440937.711831.7706
184.05540.93833.82814.06292.58825.83980.22760.2698-0.48880.32040.0601-0.63770.49710.3928-0.28770.27940.20390.07490.17850.05280.338416.36949.740335.5569
192.56061.64491.33233.6557-0.55565.61390.27060.5011-0.899-1.175-0.2023-0.64290.45610.4549-0.06830.36340.25770.16420.2151-0.04040.664113.557746.441328.1045
2010.91256.46315.06194.90236.68614.3673-0.23350.15280.8195-0.32090.09650.4959-0.3210.09890.1370.30840.22150.12320.4325-0.08610.235-9.241863.106323.2996
319.83613.0345-0.366610.8828-2.99577.5672-0.0114-0.58790.980.4579-0.58880.4888-1.4275-0.2380.60020.5651-0.0212-0.02010.2482-0.22550.37984.7569124.088234.382
329.40250.32343.15877.4627-0.67731.64350.1638-0.4817-0.65660.2684-0.2340.2459-0.0852-0.85110.07020.302-0.05360.07640.2006-0.03470.21390.888109.074631.5407
3312.225-3.91765.82196.7466-1.06498.380.46321.2947-0.8728-0.5939-0.574-0.7362-0.32330.86140.11080.3088-0.13820.10710.2712-0.10770.33316.7751108.557726.2306
346.28660.12272.0177.3669-4.87077.1135-0.5592-0.87850.18642.1044-0.0087-1.8783-1.17710.87310.56790.7342-0.0772-0.39130.5598-0.05790.718229.467296.598757.6174
357.6563-1.1311.80412.7441-2.067212.0780.26940.7591-0.5764-1.485-0.0606-0.51791.0058-0.3607-0.20880.28690.0105-0.0220.3116-0.06960.294416.123989.622737.0964
365.6946-1.4732-11.320514.3194-2.090838.7937-0.6697-0.6042-0.35491.5294-0.3583-0.17610.9891.09651.02790.1741-0.0877-0.19840.36150.02140.394821.734384.12753.8072
374.30351.56712.912219.1192-4.81554.6355-0.6546-1.50581.27253.22560.02410.0419-1.9249-0.38440.63061.22420.0776-0.26840.6029-0.18030.419619.4564104.704858.293
384.9086-2.84262.21795.6543-3.82575.1094-0.11610.27470.44320.2352-0.0639-0.6432-0.60580.56160.180.2368-0.2571-0.01810.197-0.08040.29216.9642112.535435.1038
39-0.7583-2.84023.50555.10380.10247.07230.03590.16630.02250.2411-0.003-1.0587-0.51760.8293-0.03290.3925-0.2744-0.03420.40230.01080.578423.5842107.621138.6261
408.1801-9.754814.951115.4385-8.963312.84810.1146-0.0362-0.0822-0.07710.18540.32580.8924-0.3586-0.30.1793-0.08540.10950.42090.10870.54469.270783.589745.02
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 42
2X-RAY DIFFRACTION2A43 - 78
3X-RAY DIFFRACTION3A79 - 111
4X-RAY DIFFRACTION4A112 - 150
5X-RAY DIFFRACTION5A151 - 185
6X-RAY DIFFRACTION6A186 - 207
7X-RAY DIFFRACTION7A208 - 241
8X-RAY DIFFRACTION8A242 - 304
9X-RAY DIFFRACTION9A305 - 334
10X-RAY DIFFRACTION10A335 - 370
11X-RAY DIFFRACTION11B2 - 42
12X-RAY DIFFRACTION12B43 - 78
13X-RAY DIFFRACTION13B79 - 111
14X-RAY DIFFRACTION14B112 - 150
15X-RAY DIFFRACTION15B151 - 185
16X-RAY DIFFRACTION16B186 - 207
17X-RAY DIFFRACTION17B208 - 241
18X-RAY DIFFRACTION18B242 - 304
19X-RAY DIFFRACTION19B305 - 334
20X-RAY DIFFRACTION20B335 - 370
31X-RAY DIFFRACTION31C2 - 42
32X-RAY DIFFRACTION32C43 - 78
33X-RAY DIFFRACTION33C79 - 111
34X-RAY DIFFRACTION34C112 - 150
35X-RAY DIFFRACTION35C151 - 185
36X-RAY DIFFRACTION36C186 - 207
37X-RAY DIFFRACTION37C208 - 241
38X-RAY DIFFRACTION38C242 - 304
39X-RAY DIFFRACTION39C305 - 334
40X-RAY DIFFRACTION40C335 - 370

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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

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