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- PDB-6ux8: Structure of monobody 33 MLKL N-terminal domain complex -

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Basic information

Entry
Database: PDB / ID: 6ux8
TitleStructure of monobody 33 MLKL N-terminal domain complex
Components
  • Mixed lineage kinase domain-like protein
  • Monobody
KeywordsTRANSFERASE / Protein interactions / cell death / RIPK3 / programmed necrosis / protein engineering
Function / homology
Function and homology information


execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / RIPK1-mediated regulated necrosis / TRP channels / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / RIPK1-mediated regulated necrosis / TRP channels / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Mixed lineage kinase domain-like N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBirkinshaw, R.W. / Petrie, E.J. / Murphy, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Identification of MLKL membrane translocation as a checkpoint in necroptotic cell death using Monobodies.
Authors: Petrie, E.J. / Birkinshaw, R.W. / Koide, A. / Denbaum, E. / Hildebrand, J.M. / Garnish, S.E. / Davies, K.A. / Sandow, J.J. / Samson, A.L. / Gavin, X. / Fitzgibbon, C. / Young, S.N. / ...Authors: Petrie, E.J. / Birkinshaw, R.W. / Koide, A. / Denbaum, E. / Hildebrand, J.M. / Garnish, S.E. / Davies, K.A. / Sandow, J.J. / Samson, A.L. / Gavin, X. / Fitzgibbon, C. / Young, S.N. / Hennessy, P.J. / Smith, P.P.C. / Webb, A.I. / Czabotar, P.E. / Koide, S. / Murphy, J.M.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein
B: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9776
Polymers28,7162
Non-polymers2624
Water25214
1
A: Mixed lineage kinase domain-like protein
hetero molecules

B: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9776
Polymers28,7162
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
Buried area1070 Å2
ΔGint-130 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.294, 59.418, 68.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Mixed lineage kinase domain-like protein / hMLKL


Mass: 18290.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB16
#2: Antibody Monobody


Mass: 10425.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: Monobody / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: 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

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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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG-MME 550, 0.1 M MES pH 6.5, 0.01 M Zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→68.04 Å / Num. obs: 8590 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.081 / Rrim(I) all: 0.191 / Net I/σ(I): 7 / Num. measured all: 46234 / Scaling rejects: 1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.506 / Num. measured all: 4761 / Num. unique obs: 937 / CC1/2: 0.477 / Rpim(I) all: 0.745 / Rrim(I) all: 1.688 / Net I/σ(I) obs: 1.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D0J, 4BTF

6d0j

4btf


Resolution: 2.5→44.76 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2961 468 5.48 %
Rwork0.2469 8075 -
obs0.2495 8543 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.93 Å2 / Biso mean: 65.1355 Å2 / Biso min: 31.05 Å2
Refinement stepCycle: final / Resolution: 2.5→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 4 14 1854
Biso mean--61.94 49.88 -
Num. residues----238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.860.34961370.34062619275699
2.86-3.610.32531740.286726632837100
3.61-44.760.26821570.20927932950100
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)
15.8634-1.08354.22283.7565-0.72354.76520.148-0.4220.21450.28360.05180.52280.6664-0.5182-0.13220.3388-0.06210.16060.3610.00980.5808-40.9258-32.324133.9153
28.4496-2.24463.74456.6159-1.75075.3822-0.3530.0309-0.2-0.49680.43720.1475-0.1016-0.05590.00010.4392-0.06360.00430.4249-0.14880.5147-39.9933-33.341223.4068
33.129-1.97283.26895.7091-3.01455.24160.1124-0.1823-0.0655-0.29840.0922-0.78630.76850.2012-0.09340.36290.04430.04880.4388-0.01870.6043-28.1833-33.49229.9105
40.69191.2613-0.90493.2152-1.08611.5885-0.079-0.3882-0.6688-0.13780.4148-0.4594-0.20840.2936-0.29990.3643-0.00270.10580.5165-0.00990.7683-28.8892-27.77837.1201
51.66760.9693.93431.551.73359.6051-0.43210.6141-0.7569-0.41950.3882-0.42-0.24291.03240.17160.2725-0.05210.10210.48890.12260.7359-30.2928-10.052318.2864
65.6208-0.3476-0.23063.6303-0.79054.045-0.24460.14930.185-0.6543-0.1155-0.4874-0.0988-0.03130.36510.2825-0.05270.0150.3194-0.00780.5355-29.4732-10.43926.5773
79.5652-1.45440.65477.34542.21318.78150.4494-0.19581.51910.245-0.71310.1404-0.9480.86920.32790.6499-0.0140.01430.3561-0.00850.4075-28.60520.45229.9045
86.2353-5.90770.79548.4936-2.75452.9170.2274-0.140.1120.2195-0.0689-0.25330.01470.0287-0.07580.3629-0.0968-0.02830.307-0.06840.5243-31.6688-4.11825.1923
97.9644-1.08441.76631.37881.31482.3535-0.12210.3395-0.6148-0.543-1.577-3.33450.03421.77411.85070.3873-0.17180.11120.5850.04750.7859-17.8368-15.253130.1149
107.9818-4.98458.29977.8931-4.14448.8614-0.6168-0.68690.17520.1671-0.1665-0.3255-0.28740.05650.48960.25060.00350.16090.57670.10670.7004-30.7667-0.504117.6501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )A1 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 80 )A49 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 118 )A81 - 118
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 152 )A119 - 152
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 18 )B9 - 18
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 43 )B19 - 43
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 56 )B44 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 80 )B57 - 80
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 90 )B81 - 90
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 97 )B91 - 97

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