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- PDB-2rf0: Crystal structure of human mixed lineage kinase MAP3K10 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 2rf0
TitleCrystal structure of human mixed lineage kinase MAP3K10 SH3 domain
ComponentsMitogen-activated protein kinase kinase kinase 10
KeywordsTRANSFERASE / MAP3K10 / MLK2 / SH3 domain / TKL kinase / MKN28 / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Phosphorylation / Serine/threonine-protein kinase
Function / homology
Function and homology information


: / bHLH transcription factor binding / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / smoothened signaling pathway / positive regulation of JUN kinase activity / JNK cascade / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / negative regulation of DNA-binding transcription factor activity ...: / bHLH transcription factor binding / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / smoothened signaling pathway / positive regulation of JUN kinase activity / JNK cascade / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / negative regulation of DNA-binding transcription factor activity / transcription corepressor activity / peptidyl-serine phosphorylation / protein autophosphorylation / protein kinase activity / positive regulation of apoptotic process / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / apoptotic process / signal transduction / protein homodimerization activity / ATP binding / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 10 / MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...Mitogen-activated protein (MAP) kinase kinase kinase 10 / MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUgochukwu, E. / Eswaran, J. / Elkins, J. / Keates, T. / Pike, A.C.W. / Berridge, G. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Eswaran, J. / Elkins, J. / Keates, T. / Pike, A.C.W. / Berridge, G. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human Mixed lineage kinase MAP3K10 SH3 domain.
Authors: Ugochukwu, E. / Eswaran, J. / Elkins, J. / Keates, T. / Pike, A.C.W. / Berridge, G. / Savitsky, P. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von Delft, F. / Knapp, S.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 10
B: Mitogen-activated protein kinase kinase kinase 10
C: Mitogen-activated protein kinase kinase kinase 10
D: Mitogen-activated protein kinase kinase kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0636
Polymers38,9384
Non-polymers1242
Water1,51384
1
A: Mitogen-activated protein kinase kinase kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7972
Polymers9,7351
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 10


Theoretical massNumber of molelcules
Total (without water)9,7351
Polymers9,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mitogen-activated protein kinase kinase kinase 10


Theoretical massNumber of molelcules
Total (without water)9,7351
Polymers9,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mitogen-activated protein kinase kinase kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7972
Polymers9,7351
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.680, 69.680, 103.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B
21C D

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA17 - 7828 - 89
12ALAALABB17 - 7828 - 89
21ALAALACC17 - 7828 - 89
22GLYGLYDD18 - 7829 - 89

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Components

#1: Protein
Mitogen-activated protein kinase kinase kinase 10 / Mixed lineage kinase 2 / Protein kinase MST


Mass: 9734.596 Da / Num. of mol.: 4 / Fragment: SH3 domain: Residues 13-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K10, MLK2, MST / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) phage resistant Rosetta
References: UniProt: Q02779, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium malonate, 0.1M Bis-tris-propane pH 8.5, 20.0% PEG 3350, 10.0% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00234 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00234 Å / Relative weight: 1
ReflectionResolution: 2→52.19 Å / Num. all: 19798 / Num. obs: 19798 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 21.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 4 / Rsym value: 0.739 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1OEB,1FMK

1oeb

1fmk


Resolution: 2→52.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.157 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 1013 5.1 %RANDOM
Rwork0.1889 ---
all0.19093 18749 --
obs0.19093 18749 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 8 84 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221815
X-RAY DIFFRACTIONr_bond_other_d0.0030.021142
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.932493
X-RAY DIFFRACTIONr_angle_other_deg0.84632767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2923.88972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.537158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.1880.2270
X-RAY DIFFRACTIONr_nbd_other0.2040.21161
X-RAY DIFFRACTIONr_nbtor_refined0.190.2850
X-RAY DIFFRACTIONr_nbtor_other0.0880.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0160.22
X-RAY DIFFRACTIONr_mcbond_it2.85531237
X-RAY DIFFRACTIONr_mcbond_other0.9093493
X-RAY DIFFRACTIONr_mcangle_it3.65451881
X-RAY DIFFRACTIONr_scbond_it5.1088743
X-RAY DIFFRACTIONr_scangle_it6.76711612
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A318medium positional0.190.5
1B318medium positional0.220
2C318medium positional0.150
2D318medium positional0.160
1A322loose positional0.355
1B322loose positional0.320.02
2C322loose positional0.290
2D322loose positional0.260
1A318medium thermal2.442
1B318medium thermal2.180.01
2C318medium thermal2.370
2D318medium thermal2.640
1A322loose thermal2.8610
1B322loose thermal30.03
2C322loose thermal2.650
2D322loose thermal2.780
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 73 -
Rwork0.23 1388 -
obs--100 %
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)
13.61140.2548-0.89335.2226-3.40619.83130.03090.083-0.2619-0.11920.2894-0.01841.38151.2174-0.3202-0.27560.0421-0.0335-0.04470.0416-0.1149-12.32634.99025.1929
24.8876-3.72081.10098.6585-2.24523.9591-0.3910.39080.5930.9487-0.1668-0.5278-0.53960.17770.5578-0.1885-0.2296-0.1413-0.03190.21190.0129-32.462910.27775.0857
34.73920.46680.87137.1151-0.67668.52890.02371.0348-0.0275-0.6785-0.1979-0.31450.76240.9080.1742-0.1932-0.04760.07960.1622-0.0145-0.2285-39.135-5.9575-5.981
47.22153.2278-0.39994.3161-1.336810.26520.31310.1904-0.11970.08640.06210.1219-0.2214-0.4365-0.3752-0.3478-0.03550.0373-0.09750.0261-0.2225-3.052320.2085-6.4517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 7828 - 89
2X-RAY DIFFRACTION2BB17 - 7828 - 89
3X-RAY DIFFRACTION3CC17 - 7828 - 89
4X-RAY DIFFRACTION4DD18 - 7829 - 89

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