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- PDB-5y38: Crystal structure of C7orf59-HBXIP complex -

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Basic information

Entry
Database: PDB / ID: 5y38
TitleCrystal structure of C7orf59-HBXIP complex
Components
  • Ragulator complex protein LAMTOR4
  • Ragulator complex protein LAMTOR5
KeywordsSIGNALING PROTEIN / Ragulator / LAMTOR / HBXIP / C7orf59
Function / homology
Function and homology information


positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy ...positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to lysosome / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cell size / Macroautophagy / mTORC1-mediated signalling / positive regulation of TOR signaling / positive regulation of TORC1 signaling / viral genome replication / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / response to virus / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein localization to nucleus / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / protein-containing complex / cytosol
Similarity search - Function
Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR5 / Dynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsZhang, T. / Ding, J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1
Authors: Zhang, T. / Wang, R. / Wang, Z. / Wang, X. / Wang, F. / Ding, J.
History
DepositionJul 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Ragulator complex protein LAMTOR5
B: Ragulator complex protein LAMTOR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9245
Polymers21,6362
Non-polymers2883
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-54 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.541, 58.541, 90.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ragulator complex protein LAMTOR5 / Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal ...Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5


Mass: 9622.900 Da / Num. of mol.: 1 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: O43504
#2: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 12012.636 Da / Num. of mol.: 1 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q0VGL1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.16 M ammonium sulfate, 0.08 M sodium acetate trihydrate (pH 4.6), and 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 4579 / % possible obs: 97.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.095 / Χ2: 1.403 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.8-2.95.70.4771.128198
2.9-3.026.10.3261.14196.7
3.02-3.156.60.2671.25198.9
3.15-3.326.50.1861.162198.4
3.32-3.536.60.1371.243198.3
3.53-3.86.50.1131.91197.4
3.8-4.186.60.0781.489197.7
4.18-4.796.40.0622.041196.4
4.79-6.036.40.0591.315196.3
6.03-506.10.0411.305193.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MS6

3ms6


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / SU B: 32.485 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 207 4.5 %RANDOM
Rwork0.215 ---
obs0.2168 4370 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.51 Å2 / Biso mean: 50.674 Å2 / Biso min: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0.77 Å20 Å2
2---1.55 Å20 Å2
3---2.32 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 15 10 1230
Biso mean--46.94 41.09 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191230
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9711666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36925.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.664156
X-RAY DIFFRACTIONr_chiral_restr0.3020.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021894
X-RAY DIFFRACTIONr_rigid_bond_restr6.79431230
X-RAY DIFFRACTIONr_sphericity_free11.46656
X-RAY DIFFRACTIONr_sphericity_bonded5.08351224
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 9 -
Rwork0.36 269 -
all-278 -
obs--98.93 %
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)
11.3156-1.24860.13912.7392-0.30540.4419-0.02870.0069-0.1228-0.01690.01240.0035-0.09010.0750.01630.1404-0.0106-0.00810.1539-0.00680.090324.1519-11.269411.5014
23.0507-0.233-0.72112.58080.13311.0241-0.10320.0464-0.1264-0.12640.0431-0.09420.0324-0.0160.06010.13490.0121-0.00510.1361-0.01090.098119.8377-29.03699.6399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 172
2X-RAY DIFFRACTION2B14 - 91

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