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- PDB-3iot: Huntingtin amino-terminal region with 17 Gln residues - crystal C92-b -

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Basic information

Entry
Database: PDB / ID: 3iot
TitleHuntingtin amino-terminal region with 17 Gln residues - crystal C92-b
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


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: 3.5 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 6, 2012Group: Database references / Derived calculations
Revision 1.3Jun 24, 2015Group: Source and taxonomy
Revision 1.4Jun 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 1.5Sep 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_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

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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)148,90021
Polymers147,9503
Non-polymers94918
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-32 kcal/mol
Surface area51350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.250, 101.360, 137.030
Angle α, β, γ (deg.)90.00, 91.83, 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.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
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: 2.71→50 Å / Num. obs: 40594 / Redundancy: 3 % / Rsym value: 0.09

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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: 3.5→37.36 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.854 / SU B: 90.008 / SU ML: 0.591 / Cross valid method: THROUGHOUT / ESU R Free: 0.831 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY. AUTHORS USED NCS RESTRAINTS IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29516 975 5 %RANDOM
Rwork0.24722 ---
obs0.24957 18671 69.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.46 Å2
2--0.84 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 3.5→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9177 0 18 0 9195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9612726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.92751201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15826.2400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.705151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1031512
X-RAY DIFFRACTIONr_chiral_restr0.0750.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217196
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_it0.3261.56006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57729556
X-RAY DIFFRACTIONr_scbond_it0.35333330
X-RAY DIFFRACTIONr_scangle_it0.5224.53170
X-RAY DIFFRACTIONr_rigid_bond_restr0.36939336
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.566 24 -
Rwork0.49 437 -
obs--22.15 %
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)
14.8677-0.19131.71452.9696-0.39714.02280.0522-0.14720.1249-0.01390.0239-0.13690.2351-0.0172-0.07610.11-0.00150.05360.0089-0.03680.2739-69.7853-65.910314.5382
22.95470.1246-0.00151.81110.5672.84420.0856-0.2945-0.030.1209-0.0284-0.03590.05990.0191-0.05730.13890.03630.04170.17510.01440.3019-75.4003-37.587927.2426
30.7589-1.9489-0.46645.43361.35144.2750.1325-0.08030.0395-0.4350.06950.1167-0.1002-0.3792-0.2020.05980.0044-0.0420.1020.0210.4583-77.878-62.704610.1845
49.0286-3.1879-5.24192.37681.35013.41470.13710.99450.1396-0.006-0.1689-0.1683-0.0508-0.44480.03170.150.0551-0.06810.366-0.01130.5244-73.1314-46.62416.4753
510.6759-3.4598-3.23813.24716.457414.74760.3133-0.1982-0.36170.0020.1753-0.1250.15830.2448-0.48860.2867-0.04630.00260.24960.08250.3714-60.3316-43.25832.0129
65.5171-7.08332.714125.2022.06463.48920.1284-0.1706-0.342-0.01670.11250.1478-0.10890.2406-0.2410.2648-0.26120.04710.6050.06960.3198-54.6883-36.367432.7577
73.3805-0.0041-1.29472.17851.32245.0657-0.1632-0.14530.0654-0.07930.02050.0436-0.1949-0.03630.14270.08580.0250.04110.07950.04070.3185-11.0495-63.842715.7269
82.6121-0.27020.28784.13480.6631.9134-0.05140.0332-0.1118-0.1543-0.03140.07260.22590.06240.08280.27480.05570.00520.294-0.01810.2578-35.3598-82.38048.9133
92.04360.3815-0.24992.64071.13743.98840.03630.3537-0.0019-0.6514-0.0877-0.1272-0.13690.07930.05140.24780.05850.0690.2199-0.00130.2963-8.1889-68.82417.9198
107.116-4.0133-6.211625.499413.01199.32780.26250.6438-0.06970.1719-0.62940.5361-0.096-0.70930.36690.10980.0725-0.04360.2783-0.16230.4353-25.5629-72.68836.1469
1127.803930.4606-1.866641.25984.99376.49570.6437-0.3830.24421.22020.3072-0.50850.28930.6611-0.95080.18450.14620.03410.33220.04370.508-39.6767-71.449920.7973
1217.037817.4618-0.042531.85915.60462.29290.69650.14040.68221.0836-0.44620.3290.1052-0.2396-0.25020.16940.0892-0.02730.35410.09840.5057-48.3325-68.672318.9567
133.77810.3664-1.78485.3512-0.46973.9227-0.1912-0.2630.11920.2644-0.02-0.0121-0.1947-0.23550.21120.19150.0699-0.06140.376-0.09760.2264-42.68-17.578533.7216
142.80420.62490.11493.02170.5052.42090.0812-0.18730.0470.1512-0.0815-0.0451-0.02180.02180.00030.246-0.03520.02830.2417-0.03370.2346-13.2599-28.114230.6794
159.16611.8107-3.81872.2715-0.58273.79960.0730.34810.5608-0.08250.0310.1058-0.6846-0.1315-0.10410.38250.0627-0.03110.2167-0.07850.3891-37.3116-9.777630.8949
1611.95175.94321.07494.2292-1.26864.3107-0.68280.6687-0.1591-0.49380.3088-0.1747-0.1958-0.2040.3740.15790.04440.06150.2297-0.08940.4454-24.8838-21.700226.1908
1732.9431-9.38275.05216.7482-2.35575.03470.4494-0.047-0.2418-0.041-0.30850.48741.0196-0.5098-0.14090.345-0.07930.00310.1497-0.01160.3202-23.767-41.145832.7687
1828.2923-1.10225.88484.66710.547610.72810.66540.3215-0.4816-0.37670.09930.340.5832-0.2565-0.76470.47070.00830.04090.0472-0.03090.2897-21.2197-47.830927.7004
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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