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- PDB-4rqm: Crystal structure of the SeMET BICC1 SAM Domain R924E mutant -

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Basic information

Entry
Database: PDB / ID: 4rqm
TitleCrystal structure of the SeMET BICC1 SAM Domain R924E mutant
ComponentsProtein bicaudal C homolog 1
KeywordsPROTEIN BINDING / SAM domain / protein-protein interaction domain / polymerization domain / Polymerization / P-bodies
Function / homology
Function and homology information


determination of left/right symmetry / kidney development / negative regulation of canonical Wnt signaling pathway / heart development / RNA binding / cytoplasm
Similarity search - Function
BICC1, SAM domain / : / : / : / Protein bicaudal C homolog 1, KH-like domain / Transcription Factor, Ets-1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) ...BICC1, SAM domain / : / : / : / Protein bicaudal C homolog 1, KH-like domain / Transcription Factor, Ets-1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SAM domain (Sterile alpha motif) / K Homology domain, type 1 superfamily / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / K Homology domain / K homology RNA-binding domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein bicaudal C homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsLeettola, C.N. / Cascio, D. / Bowie, J.U.
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.
Authors: Rothe, B. / Leettola, C.N. / Leal-Esteban, L. / Cascio, D. / Fortier, S. / Isenschmid, M. / Bowie, J.U. / Constam, D.B.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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.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.value / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein bicaudal C homolog 1
B: Protein bicaudal C homolog 1
C: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4414
Polymers24,3753
Non-polymers651
Water72140
1
A: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)8,1251
Polymers8,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein bicaudal C homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1902
Polymers8,1251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein bicaudal C homolog 1


Theoretical massNumber of molelcules
Total (without water)8,1251
Polymers8,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.810, 64.430, 70.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSASNASNchain AAA874 - 9366 - 68
2ASPASPLYSLYSchain BBB877 - 9359 - 67
3ASPASPARGARGchain CCC877 - 9389 - 70

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Components

#1: Protein Protein bicaudal C homolog 1 / Bic-C


Mass: 8125.065 Da / Num. of mol.: 3 / Fragment: SAM domain of BICC1, UNP residues 870-939 / Mutation: R924E
Source method: isolated from a genetically manipulated source
Details: SER 869 is an artifact of cloning / Source: (gene. exp.) Homo sapiens (human) / Gene: BICC1 / Plasmid: pHis-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9H694
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% PEG-550 MME, 100mM MES, 5mM zinc sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.75→47.6 Å / Num. obs: 22189 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 28.95 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 10.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.80.4232.05192.3
1.8-1.840.3832.6198.6
1.84-1.90.3153.31198.1
1.9-1.960.2694.11197
1.96-2.020.2045.51193.4
2.02-2.090.1477.45193.5
2.09-2.170.119.52195.3
2.17-2.260.09910.74192.8
2.26-2.360.07712.15193
2.36-2.480.0712.97192.9
2.48-2.610.06213.76187.8
2.61-2.770.05315.86191.3
2.77-2.960.05116.57191.3
2.96-3.20.04917.48190.3
3.2-3.50.04718.47189.5
3.5-3.910.04318.4186.8
3.91-4.520.04320.04189.4
4.52-5.530.04319.84190.8
5.53-7.830.0419.09189.5
7.83-47.60.04621.18189.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.75→47.603 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 1058 4.87 %
Rwork0.2297 --
obs0.2316 21730 97.93 %
all-21727 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.7126 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 1 40 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081455
X-RAY DIFFRACTIONf_angle_d1.1231961
X-RAY DIFFRACTIONf_dihedral_angle_d12.057541
X-RAY DIFFRACTIONf_chiral_restr0.049237
X-RAY DIFFRACTIONf_plane_restr0.005250
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A794X-RAY DIFFRACTION7.722TORSIONAL
12B794X-RAY DIFFRACTION7.722TORSIONAL
13C794X-RAY DIFFRACTION7.722TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.82970.28961300.25292398X-RAY DIFFRACTION93
1.8297-1.92610.33961080.24692485X-RAY DIFFRACTION95
1.9261-2.04680.2892990.24942542X-RAY DIFFRACTION97
2.0468-2.20480.26381460.22592570X-RAY DIFFRACTION99
2.2048-2.42670.24691380.21722609X-RAY DIFFRACTION100
2.4267-2.77780.23231360.22762620X-RAY DIFFRACTION100
2.7778-3.49960.29631590.24372644X-RAY DIFFRACTION100
3.4996-47.62080.25941420.22152804X-RAY DIFFRACTION100
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)
14.89336.76980.09269.38510.8355.0098-0.14610.8439-0.6452-0.37380.3021-0.30650.00980.3479-0.08640.25380.08140.01950.4058-0.10.405918.88354.3476-3.7351
28.5182-1.55465.51658.294-2.22633.69990.5196-0.1018-0.8001-0.530.0740.5620.9908-0.6038-0.45020.2707-0.0069-0.05070.3124-0.03440.304510.83278.14012.6775
34.7169-4.88615.33697.1834-4.65426.12050.02420.52410.3734-0.3442-0.1790.10170.05140.18230.17820.1309-0.0221-0.01950.29960.00910.233516.95315.62021.3112
41.2381.0251.12643.13581.69057.25920.0656-0.2259-0.28931.77570.7246-0.7435-0.41820.59880.06081.05250.2063-0.19410.36070.08870.193123.578815.014824.0705
56.67463.56791.04418.99830.05027.7154-0.1346-0.09430.55490.67570.1940.31340.0917-0.1977-0.10630.28960.04830.00270.2508-0.03740.20218.808219.390915.7907
67.34996.8204-4.42929.6163-6.15565.25450.2915-0.0493-0.24720.7685-0.3116-0.3438-0.0950.0322-0.04590.57940.04040.01970.2746-0.04650.248418.662526.711622.1003
76.40291.112-4.09948.6853-0.36665.7223-0.3654-0.4449-0.33450.848-0.2928-0.40751.09430.41490.63620.4991-0.03280.10220.36010.0420.2775.561724.356138.9214
88.1946-0.31820.5467.41290.46789.0245-0.33440.1899-0.5612-0.0440.02510.08450.7571-0.42890.30590.3393-0.0330.16510.328-0.12060.27386.006630.146330.1398
98.3976.27293.1256.6872.70292.14950.0184-0.29920.42950.1837-0.30770.65910.1834-0.08010.30810.2246-0.00510.10580.243-0.0420.39682.544436.461936.3793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 874:898 )A874 - 898
2X-RAY DIFFRACTION2( CHAIN A AND RESID 899:918 )A899 - 918
3X-RAY DIFFRACTION3( CHAIN A AND RESID 919:936 )A919 - 936
4X-RAY DIFFRACTION4( CHAIN B AND RESID 877:898 )B877 - 898
5X-RAY DIFFRACTION5( CHAIN B AND RESID 899:918 )B899 - 918
6X-RAY DIFFRACTION6( CHAIN B AND RESID 919:935 )B919 - 935
7X-RAY DIFFRACTION7( CHAIN C AND RESID 877:898 )C877 - 898
8X-RAY DIFFRACTION8( CHAIN C AND RESID 899:918 )C899 - 918
9X-RAY DIFFRACTION9( CHAIN C AND RESID 919:935 )C919 - 935

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