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- PDB-3lrh: Structure of anti-huntingtin VL domain in complex with huntingtin... -

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Basic information

Entry
Database: PDB / ID: 3lrh
TitleStructure of anti-huntingtin VL domain in complex with huntingtin peptide
Components
  • Huntingtin
  • anti-huntingtin VL domain
KeywordsIMMUNE SYSTEM / Huntington's disease / Huntingtin / Variable light chain domain / Intrabody / Immunoglobulin
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 / establishment of mitotic spindle orientation / dynactin binding / 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 / transmembrane transporter binding / early endosome / positive regulation of apoptotic process / axon / apoptotic process / dendrite / 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 / Armadillo-like helical / Armadillo-type fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchiefner, A. / Chatwell, L. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A Disulfide-Free Single-Domain V(L) Intrabody with Blocking Activity towards Huntingtin Reveals a Novel Mode of Epitope Recognition.
Authors: Schiefner, A. / Chatwell, L. / Korner, J. / Neumaier, I. / Colby, D.W. / Volkmer, R. / Wittrup, K.D. / Skerra, A.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Jan 11, 2012Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-huntingtin VL domain
B: Huntingtin
C: anti-huntingtin VL domain
D: Huntingtin
E: anti-huntingtin VL domain
F: Huntingtin
G: anti-huntingtin VL domain
H: Huntingtin
I: anti-huntingtin VL domain
J: Huntingtin
K: anti-huntingtin VL domain
L: Huntingtin
M: anti-huntingtin VL domain
N: Huntingtin
O: anti-huntingtin VL domain
P: Huntingtin


Theoretical massNumber of molelcules
Total (without water)116,40016
Polymers116,40016
Non-polymers00
Water3,675204
1
A: anti-huntingtin VL domain
B: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-12 kcal/mol
Surface area6480 Å2
MethodPISA
2
C: anti-huntingtin VL domain
D: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-13 kcal/mol
Surface area6530 Å2
MethodPISA
3
E: anti-huntingtin VL domain
F: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area6950 Å2
MethodPISA
4
G: anti-huntingtin VL domain
H: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-12 kcal/mol
Surface area6610 Å2
MethodPISA
5
I: anti-huntingtin VL domain
J: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-12 kcal/mol
Surface area6600 Å2
MethodPISA
6
K: anti-huntingtin VL domain
L: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area6430 Å2
MethodPISA
7
M: anti-huntingtin VL domain
N: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-12 kcal/mol
Surface area6560 Å2
MethodPISA
8
O: anti-huntingtin VL domain
P: Huntingtin


Theoretical massNumber of molelcules
Total (without water)14,5502
Polymers14,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-13 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.090, 89.660, 95.000
Angle α, β, γ (deg.)90.00, 99.45, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains 8 complexes of anti-huntingtin VL domain in complex with the huntingtin fragment 5-18.

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Components

#1: Antibody
anti-huntingtin VL domain


Mass: 12860.970 Da / Num. of mol.: 8 / Fragment: anti-huntingtin VL domain / Mutation: G112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Phage display library / synthetic / Gene: VL12.3 / Plasmid: pASK75(T7RBS)his / Production host: Escherichia coli (E. coli) / Strain (production host): JM83
#2: Protein/peptide
Huntingtin / / Huntington disease protein / HD protein


Mass: 1689.003 Da / Num. of mol.: 8 / Fragment: huntingtin peptide / Source method: obtained synthetically
Details: The huntingtin fragment 5-18 was obtained by peptide synthesis. This sequence occurs naturally in humans.
References: UniProt: P42858
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 10 % PEG600, 0.1 mM potassium phosphate dibasic/citric acid, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 3, 2006
RadiationMonochromator: Osmic confocal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 24090 / % possible obs: 88.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.1 / % possible all: 92

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LRG

3lrg


Resolution: 2.6→19.86 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.827 / SU B: 33.014 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27804 1221 5.1 %RANDOM
Rwork0.21564 ---
obs0.21885 22868 88.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.953 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å2-0.34 Å2
2--3.5 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7448 0 0 204 7652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0227584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8281.95710298
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4595975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31124.904314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.888151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6221540
X-RAY DIFFRACTIONr_chiral_restr0.0540.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215732
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_it01.54907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it02.57866
X-RAY DIFFRACTIONr_scbond_it0.0033.52677
X-RAY DIFFRACTIONr_scangle_it0.005102432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 101 -
Rwork0.248 1720 -
obs--91.69 %
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)
11.7939-0.64520.19781.4392-0.27462.54430.0198-0.0697-0.0356-0.01280.02580.074-0.0686-0.0141-0.04560.0537-0.0121-0.02150.06050.00210.08568.4383-23.5116-49.192
25.58491.87660.53440.91421.935910.94750.0403-0.2048-0.46930.13820.0162-0.16810.79850.5241-0.05650.19870.05510.03330.06010.04970.189921.2161-29.5282-48.8554
32.6265-0.135-0.05652.05870.552.21920.0571-0.14850.05250.07750.0515-0.1553-0.02060.0914-0.10850.0904-0.03060.01070.11310.00520.0843-15.2189-14.5662-45.5888
42.8088-3.91445.32389.2127-3.911413.5789-0.3128-0.4377-0.00780.57150.19220.288-1.044-1.26570.12050.3328-0.03310.20460.2178-0.05950.3323-27.7097-8.3725-44.8704
52.29310.9342-0.48092.043-0.22442.25360.0458-0.0133-0.15140.0548-0.0343-0.20550.22940.2271-0.01140.14810.0323-0.0360.0755-0.02140.0707-16.2325-25.1427-68.2808
610.01-4.81351.85043.0655-0.632919.56430.26150.7971-0.7542-0.2763-0.0720.44851.1371-0.6412-0.18950.3164-0.06770.07760.2317-0.01340.1763-29.4926-30.5774-68.2873
71.945-0.38360.23361.1094-1.29043.74570.00320.0333-0.05250.12350.00910.1299-0.0406-0.0654-0.01230.067-0.01-0.00880.0738-0.02060.07297.6531-15.7266-73.0683
87.85775.12486.86584.68068.634419.01990.42520.09080.09040.01630.3898-0.2896-0.28851.0525-0.8150.25680.04020.0790.22380.03720.354120.549-9.6217-73.8208
91.6446-0.76110.261.1889-0.50971.7829-0.0865-0.0873-0.0059-0.07160.02230.0785-0.03920.06270.06430.0441-0.0062-0.00170.0621-0.00060.062.0171-27.6308-1.8606
103.51391.89680.57361.72794.94330.6695-0.3531-0.3568-0.30210.0157-0.1051-0.09591.22860.69820.45830.11430.04190.05370.19080.02750.17914.9799-33.2478-3.222
112.25521.0079-0.42581.30611.0481.9484-0.0736-0.03510.02220.00550.05250.04570.07060.0270.02110.05650.0135-0.02370.08330.02640.0239-21.4087-19.286-0.2885
126.10050.70282.41563.2939-7.522120.2434-0.0607-0.29160.67450.55360.1990.2962-1.4624-1.037-0.13830.12620.127-0.00940.2501-0.12180.1997-33.567-13.11892.401
131.93990.9114-0.08361.13970.58552.1787-0.03930.0134-0.0930.0766-0.0435-0.11880.0709-0.04510.08280.0359-0.0068-0.00480.08620.02230.0574-24.8706-26.3263-23.8486
147.5091-2.90090.72552.7953-6.38822.68170.10450.4351-0.4852-0.3910.00910.24181.3355-0.8819-0.11360.0939-0.06110.02650.2578-0.05270.1566-37.958-32.2283-22.8471
155.2089-0.7939-0.26323.8903-1.09231.75030.10260.34620.2277-0.1386-0.04040.0564-0.0349-0.0037-0.06220.0397-0.0046-0.0030.11540.01640.043-1.5508-17.6404-24.3145
168.41155.8844-2.14234.52991.396839.9139-0.0465-0.2103-0.3182-0.1863-0.3099-0.59-1.19861.25610.35650.08910.07910.15980.29680.38320.819110.6808-11.525-26.5984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 110
2X-RAY DIFFRACTION2B5 - 18
3X-RAY DIFFRACTION3C2 - 110
4X-RAY DIFFRACTION4D5 - 18
5X-RAY DIFFRACTION5E-1 - 111
6X-RAY DIFFRACTION6F5 - 18
7X-RAY DIFFRACTION7G2 - 110
8X-RAY DIFFRACTION8H5 - 18
9X-RAY DIFFRACTION9I2 - 111
10X-RAY DIFFRACTION10J5 - 18
11X-RAY DIFFRACTION11K2 - 110
12X-RAY DIFFRACTION12L5 - 18
13X-RAY DIFFRACTION13M2 - 111
14X-RAY DIFFRACTION14N5 - 18
15X-RAY DIFFRACTION15O-1 - 110
16X-RAY DIFFRACTION16P5 - 18

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