[English] 日本語
Yorodumi
- PDB-4rqm: Crystal structure of the SeMET BICC1 SAM Domain R924E mutant -

+
Open data


ID or keywords:

Loading...

-
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 / : / : / : / 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 ...BICC1, SAM 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA874 - 936
211chain BB877 - 935
311chain CC877 - 938

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more