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- PDB-6cqd: Crystal structure of HPK1 in complex with ATP analogue (AMPPNP) -

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Basic information

Entry
Database: PDB / ID: 6cqd
TitleCrystal structure of HPK1 in complex with ATP analogue (AMPPNP)
ComponentsMitogen-activated protein kinase kinase kinase kinase 1
KeywordsTRANSFERASE / Protein kinase
Function / homology
Function and homology information


MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAP kinase kinase kinase kinase activity / cellular response to phorbol 13-acetate 12-myristate / JNK cascade / peptidyl-serine phosphorylation / cell population proliferation / positive regulation of MAPK cascade / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.12 Å
AuthorsWu, P. / Lehoux, I. / Franke, Y. / Mortara, K. / Wang, W.
CitationJournal: Structure / Year: 2019
Title: Hematopoietic Progenitor Kinase-1 Structure in a Domain-Swapped Dimer.
Authors: Wu, P. / Sneeringer, C.J. / Pitts, K.E. / Day, E.S. / Chan, B.K. / Wei, B. / Lehoux, I. / Mortara, K. / Li, H. / Wu, J. / Franke, Y. / Moffat, J.G. / Grogan, J.L. / Heffron, T.P. / Wang, W.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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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 kinase 1
B: Mitogen-activated protein kinase kinase kinase kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4987
Polymers66,4132
Non-polymers1,0855
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-72 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.886, 51.882, 107.500
Angle α, β, γ (deg.)90.00, 131.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 1 / HKP1 / Hematopoietic progenitor kinase / MAPK/ERK kinase kinase kinase 1 / MEKKK 1


Mass: 33206.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K1, HPK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q92918, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 12% PEG8000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 35007 / % possible obs: 99.9 % / Redundancy: 3.3 % / Net I/σ(I): 8.8
Reflection shellResolution: 2.12→2.127 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.12→46.987 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 30.01
RfactorNum. reflection% reflection
Rfree0.2498 3303 5.08 %
Rwork0.2034 --
obs0.2059 34951 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→46.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 65 217 4854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054749
X-RAY DIFFRACTIONf_angle_d0.8476415
X-RAY DIFFRACTIONf_dihedral_angle_d14.4861763
X-RAY DIFFRACTIONf_chiral_restr0.03719
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.15030.4061300.32432527X-RAY DIFFRACTION94
2.1503-2.18240.35041040.29662610X-RAY DIFFRACTION95
2.1824-2.21650.30081460.29262497X-RAY DIFFRACTION96
2.2165-2.25280.3311660.2842622X-RAY DIFFRACTION95
2.2528-2.29170.32981200.27772523X-RAY DIFFRACTION94
2.2917-2.33340.35971410.26152494X-RAY DIFFRACTION92
2.3334-2.37820.32441580.27052437X-RAY DIFFRACTION92
2.3782-2.42680.28461110.24352580X-RAY DIFFRACTION95
2.4268-2.47950.33091380.25052522X-RAY DIFFRACTION96
2.4795-2.53720.30211210.24832607X-RAY DIFFRACTION96
2.5372-2.60070.29661350.23792636X-RAY DIFFRACTION97
2.6007-2.6710.33621190.24532628X-RAY DIFFRACTION97
2.671-2.74960.28941190.23672618X-RAY DIFFRACTION97
2.7496-2.83830.29551580.24632588X-RAY DIFFRACTION97
2.8383-2.93970.28551470.24372561X-RAY DIFFRACTION97
2.9397-3.05740.28691450.24172637X-RAY DIFFRACTION97
3.0574-3.19650.30371160.23462549X-RAY DIFFRACTION96
3.1965-3.3650.33491200.21842523X-RAY DIFFRACTION93
3.365-3.57580.26161320.19512614X-RAY DIFFRACTION96
3.5758-3.85170.20971510.17872570X-RAY DIFFRACTION96
3.8517-4.23910.19751470.15142622X-RAY DIFFRACTION98
4.2391-4.8520.18551580.1332618X-RAY DIFFRACTION98
4.852-6.11090.18471650.1572523X-RAY DIFFRACTION95
6.1109-46.99810.17151560.15032654X-RAY DIFFRACTION99
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)
10.38430.20340.0040.2132-0.14430.5661-0.161-0.04680.05020.11830.0745-0.0592-0.5241-0.05800.34040.0688-0.05130.2227-0.01420.308114.43489.585212.8207
20.6434-0.19320.35520.9380.09441.80270.0332-0.0403-0.02450.0958-0.05820.05120.0325-0.1285-00.1432-0.01920.00110.1518-0.00940.184418.5789-10.227426.9589
30.17720.05930.14030.42520.02940.38930.03630.12780.0231-0.35960.1569-0.0654-0.2569-0.20390.00010.3650.07720.03570.52240.0710.388712.769124.908859.5205
40.5888-0.55250.2566-0.21620.31761.1237-0.1015-0.06840.0713-0.1237-0.0165-0.01010.6599-0.0044-0.13070.41610.03220.06620.21290.02990.178725.43824.121161.2632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 2:93
2X-RAY DIFFRACTION2chain A and resi 94:294
3X-RAY DIFFRACTION3chain B and resi 4:93
4X-RAY DIFFRACTION4chain B and resi 94:294

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