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- PDB-7mk7: Augmentor domain of augmentor-beta -

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Basic information

Entry
Database: PDB / ID: 7mk7
TitleAugmentor domain of augmentor-beta
ComponentsALK and LTK ligand 1,Maltodextrin-binding protein
KeywordsCYTOKINE / cell signaling
Function / homology
Function and homology information


positive regulation of ERK5 cascade / receptor signaling protein tyrosine kinase activator activity / Signaling by LTK / Signaling by ALK / transmembrane receptor protein tyrosine kinase activator activity / carbohydrate transmembrane transporter activity / cell surface receptor protein tyrosine kinase signaling pathway / cytokine activity / receptor tyrosine kinase binding / positive regulation of neuron projection development ...positive regulation of ERK5 cascade / receptor signaling protein tyrosine kinase activator activity / Signaling by LTK / Signaling by ALK / transmembrane receptor protein tyrosine kinase activator activity / carbohydrate transmembrane transporter activity / cell surface receptor protein tyrosine kinase signaling pathway / cytokine activity / receptor tyrosine kinase binding / positive regulation of neuron projection development / periplasmic space / positive regulation of ERK1 and ERK2 cascade / extracellular space / extracellular region / plasma membrane
Similarity search - Function
ALK and LTK ligand 1/2 / ALK and LTK ligand 1/2 / 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
Similarity search - Domain/homology
alpha-maltose / Maltodextrin-binding protein / ALK and LTK ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42815184462 Å
AuthorsKrimmer, S.G. / Reshetnyak, A.V. / Puleo, D.E. / Schlessinger, J.
CitationJournal: Nature / Year: 2021
Title: Structural basis for ligand reception by anaplastic lymphoma kinase.
Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / ...Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / Alvarado, D. / Lemmon, M.A. / Schlessinger, J. / Klein, D.E.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALK and LTK ligand 1,Maltodextrin-binding protein
B: ALK and LTK ligand 1,Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9264
Polymers93,2422
Non-polymers6852
Water25214
1
A: ALK and LTK ligand 1,Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9632
Polymers46,6211
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALK and LTK ligand 1,Maltodextrin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9632
Polymers46,6211
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.569, 56.775, 94.408
Angle α, β, γ (deg.)75.598, 77.348, 61.785
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein ALK and LTK ligand 1,Maltodextrin-binding protein / Augmentor beta / AUG-beta / Protein FAM150A


Mass: 46620.910 Da / Num. of mol.: 2
Mutation: D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V
Source method: isolated from a genetically manipulated source
Details: Augmentor beta residues 60-129 followed by C-terminal MBP tag
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ALKAL1, malE / Production host: Escherichia coli (E. coli) / References: UniProt: Q6UXT8, UniProt: A0A2Y0TBT9
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 / Details: 0.1 M sodium citrate pH 4.9, 16% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.428→50 Å / Num. obs: 33843 / % possible obs: 94.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.3076599347 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.131 / Rsym value: 0.121 / Net I/σ(I): 10.12
Reflection shellResolution: 2.428→2.57 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 5220 / CC1/2: 0.806 / Rsym value: 1.017 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.42815184462→46.8693459097 Å / SU ML: 0.443242208387 / Cross valid method: FREE R-VALUE / σ(F): 1.91362251049 / Phase error: 33.5049052651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272785621752 1688 5.00459545198 %
Rwork0.214388970917 32041 -
obs0.21730694854 33729 94.7763290997 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.8147726441 Å2
Refinement stepCycle: LAST / Resolution: 2.42815184462→46.8693459097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 46 14 5441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004929201102315587
X-RAY DIFFRACTIONf_angle_d0.7465644770477689
X-RAY DIFFRACTIONf_chiral_restr0.0474023497872897
X-RAY DIFFRACTIONf_plane_restr0.00480810271838982
X-RAY DIFFRACTIONf_dihedral_angle_d11.73286291033248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4282-2.49960.5096436492931270.4215333553272394X-RAY DIFFRACTION85.0252951096
2.4996-2.58030.3356467584381430.3185073831572723X-RAY DIFFRACTION96.1099932931
2.5803-2.67250.3549428582761410.2918518424852671X-RAY DIFFRACTION95.9072305593
2.6725-2.77950.3112663030821430.2766313004512712X-RAY DIFFRACTION95.9986550101
2.7795-2.9060.3209696746421400.2725854575992665X-RAY DIFFRACTION95.8319098053
2.906-3.05910.3354692284881450.2724103479612751X-RAY DIFFRACTION96.6622162884
3.0591-3.25080.327447055791440.2593785212542724X-RAY DIFFRACTION96.4033613445
3.2508-3.50170.2813866397321420.2231857376662693X-RAY DIFFRACTION95.2620967742
3.5017-3.85390.2278815404551370.1947531533092626X-RAY DIFFRACTION93.6610169492
3.8539-4.41120.2387272881231440.1804981796752731X-RAY DIFFRACTION96.5413028878
4.4112-5.55620.2511905619561380.1788736313582636X-RAY DIFFRACTION93.7795807978
5.5562-46.8690.2458788359571440.1859513795592715X-RAY DIFFRACTION96.1654894046
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)
11.1107167435-2.20249332672-1.923702748187.224771878895.168811004053.97344449440.13193304947-0.06751558491880.242697883796-0.5423194797860.321423765109-0.6133704906460.08378130384760.153157134611-0.4372114933150.537328225920.03833696227650.02251403935940.418320212080.163204913490.75244339767857.650083775774.9469941033106.551601419
22.55528626186-1.49703233794-0.5449840945043.372847590910.2759497587241.76564874855-0.323314868048-0.1410536177070.1814898862180.4627726225710.323493598267-0.258862237435-0.0686999590212-0.03070304475160.01377099893250.4199422224530.120233960991-0.05454912616070.3612929369920.1674395297620.62923787675242.6199339341101.553427694126.661765008
30.1551901016510.09793463342450.2806312811268.23167012116.53524026625.6614866372-0.1090238748960.0106747267624-0.0203330482807-0.2553268748050.744321675109-0.778329205672-0.1892870091230.476738213828-0.65516757990.439368420795-0.04397406901450.08201127204890.4574910956450.1385858553020.76844174884162.640334311253.929653691788.4232710193
42.369323227721.29935245729-0.4258173854852.77819176835-0.4214308188211.88753452141-0.4016405458830.15856355502-0.168225279422-0.7842654809820.375990628251-0.224052170815-0.01176189414730.03995938554510.00160570232520.69938791292-0.1712983303990.09989238495280.3971630447110.1238516987250.63618602517448.840540073120.238428394668.2758511754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 475 )
3X-RAY DIFFRACTION3chain 'B' and (resid 85 through 140 )
4X-RAY DIFFRACTION4chain 'B' and (resid 141 through 475 )

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