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- PDB-3hwj: Crystal structure of the second PHR domain of Mouse Myc-binding p... -

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Basic information

Entry
Database: PDB / ID: 3hwj
TitleCrystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2)
ComponentsE3 ubiquitin-protein ligase MYCBP2
KeywordsLIGASE / Myc-binding protein 2 / MYCBP2 / PHR proteins / PHR domain / Probable E3 ubiquitin-protein ligase MYCBP2 / Protein Associated with Myc / PAM / Phr1 / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Alternative splicing / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation pathway / Zinc / Zinc-finger / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / cell morphogenesis involved in neuron differentiation / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / motor neuron axon guidance / neuromuscular process / regulation of cytoskeleton organization / protein K48-linked ubiquitination ...RCR-type E3 ubiquitin transferase / regulation of axon guidance / regulation of synaptic assembly at neuromuscular junction / cell morphogenesis involved in neuron differentiation / branchiomotor neuron axon guidance / central nervous system projection neuron axonogenesis / motor neuron axon guidance / neuromuscular process / regulation of cytoskeleton organization / protein K48-linked ubiquitination / guanyl-nucleotide exchange factor activity / positive regulation of protein ubiquitination / axon guidance / circadian regulation of gene expression / negative regulation of protein catabolic process / small GTPase binding / regulation of protein localization / ubiquitin protein ligase activity / microtubule cytoskeleton / protein ubiquitination / axon / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PHR domain / PHR / PHR domain superfamily / PHR domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain ...PHR domain / PHR / PHR domain superfamily / PHR domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Ring finger / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MYCBP2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSampathkumar, P. / Ozyurt, S.A. / Wasserman, S.R. / Miller, S.A. / Bain, K.T. / Rutter, M.E. / Gheyi, T. / Klemke, R.L. / Atwell, S. / Sauder, J.M. ...Sampathkumar, P. / Ozyurt, S.A. / Wasserman, S.R. / Miller, S.A. / Bain, K.T. / Rutter, M.E. / Gheyi, T. / Klemke, R.L. / Atwell, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structures of PHR domains from Mus musculus Phr1 (Mycbp2) explain the loss-of-function mutation (Gly1092-->Glu) of the C. elegans ortholog RPM-1.
Authors: Sampathkumar, P. / Ozyurt, S.A. / Miller, S.A. / Bain, K.T. / Rutter, M.E. / Gheyi, T. / Abrams, B. / Wang, Y. / Atwell, S. / Luz, J.G. / Thompson, D.A. / Wasserman, S.R. / Emtage, J.S. / ...Authors: Sampathkumar, P. / Ozyurt, S.A. / Miller, S.A. / Bain, K.T. / Rutter, M.E. / Gheyi, T. / Abrams, B. / Wang, Y. / Atwell, S. / Luz, J.G. / Thompson, D.A. / Wasserman, S.R. / Emtage, J.S. / Park, E.C. / Rongo, C. / Jin, Y. / Klemke, R.L. / Sauder, J.M. / Burley, S.K.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MYCBP2
B: E3 ubiquitin-protein ligase MYCBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1815
Polymers37,9472
Non-polymers2343
Water2,234124
1
A: E3 ubiquitin-protein ligase MYCBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0522
Polymers18,9741
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 ubiquitin-protein ligase MYCBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1303
Polymers18,9741
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.877, 99.922, 83.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein E3 ubiquitin-protein ligase MYCBP2 / Myc-binding protein 2 / MYCBP-2 / Protein associated with Myc / Pam/highwire/rpm-1 protein


Mass: 18973.525 Da / Num. of mol.: 2 / Fragment: Second PHR domain: UNP Q7TPH6 residues 1685-1845
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mycbp2, Pam, Phr1 / Plasmid: BC-PSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL
References: UniProt: Q7TPH6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Compound detailsONLY THE A CONFORMER FORMS A DISULFIDE BOND.
Sequence detailsTHE AUTHORS STATE THAT THE PRESENCE OF ARG IS CONFIRMED BY THE ELECTRON DENSITY MAPS. ALSO MOST ...THE AUTHORS STATE THAT THE PRESENCE OF ARG IS CONFIRMED BY THE ELECTRON DENSITY MAPS. ALSO MOST OTHER PAM HOMOLOGUES LIKE HUMAN, DOG, CHICKEN, FISH, ETC. HAVE AN ARG AT THIS POSITION.

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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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2000mM DL Malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 13, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→42.8 Å / Num. obs: 18914 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.59 Å2 / Rsym value: 0.13 / Net I/σ(I): 8.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2732 / Rsym value: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly ala based on the PDB Code 3GBW

3gbw


Resolution: 2.25→31.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.639 / SU ML: 0.167 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 972 5.1 %RANDOM
Rwork0.198 ---
obs0.201 18890 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.17 Å2 / Biso mean: 43.016 Å2 / Biso min: 12.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.25→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 12 132 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222365
X-RAY DIFFRACTIONr_bond_other_d0.0010.021553
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9483227
X-RAY DIFFRACTIONr_angle_other_deg0.9673.0023773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1515312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51823.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6411518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2060.2426
X-RAY DIFFRACTIONr_nbd_other0.2020.21629
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21126
X-RAY DIFFRACTIONr_nbtor_other0.0910.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.23
X-RAY DIFFRACTIONr_mcbond_it1.171.51544
X-RAY DIFFRACTIONr_mcbond_other0.2131.5631
X-RAY DIFFRACTIONr_mcangle_it1.80322443
X-RAY DIFFRACTIONr_scbond_it2.5223936
X-RAY DIFFRACTIONr_scangle_it3.8424.5779
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 81 -
Rwork0.239 1303 -
all-1384 -
obs--100 %

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