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- PDB-7ajl: Cyrstal structure of CYRI-B/Fam49B -

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Basic information

Entry
Database: PDB / ID: 7ajl
TitleCyrstal structure of CYRI-B/Fam49B
ComponentsCYFIP-related Rac1 interactor B
KeywordsCYTOSOLIC PROTEIN / Rac1 competitor / actin regulation / Scar/WAVE inhibitor
Function / homology
Function and homology information


MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / cellular response to molecule of bacterial origin / Platelet degranulation / negative regulation of actin filament polymerization / regulation of chemotaxis / regulation of establishment of cell polarity / regulation of mitochondrial fission / positive regulation of memory T cell activation / regulation of cell migration ...MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / cellular response to molecule of bacterial origin / Platelet degranulation / negative regulation of actin filament polymerization / regulation of chemotaxis / regulation of establishment of cell polarity / regulation of mitochondrial fission / positive regulation of memory T cell activation / regulation of cell migration / cilium / small GTPase binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / positive regulation of type II interferon production / mitochondrion / membrane
Similarity search - Function
CYFIP-related Rac1 interactor / CYRIA/CYRIB, Rac1 binding domain / CYRIA/CYRIB Rac1 binding domain
Similarity search - Domain/homology
CYFIP-related Rac1 interactor B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsYelland, T. / Anh, H. / Insall, R. / Machesky, L. / Ismail, S.
Funding support1items
OrganizationGrant numberCountry
Cancer Research UK
CitationJournal: Structure / Year: 2021
Title: Structural Basis of CYRI-B Direct Competition with Scar/WAVE Complex for Rac1.
Authors: Yelland, T. / Le, A.H. / Nikolaou, S. / Insall, R. / Machesky, L. / Ismail, S.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: CYFIP-related Rac1 interactor B
BBB: CYFIP-related Rac1 interactor B


Theoretical massNumber of molelcules
Total (without water)68,7992
Polymers68,7992
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, pulldown
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-7 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.731, 166.686, 45.131
Angle α, β, γ (deg.)90.000, 112.343, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein CYFIP-related Rac1 interactor B / Protein FAM49B


Mass: 34399.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cyrib, Cyri, Fam49b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q921M7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M carboxylic acid, 8% MPD_P1K_P33 0.1M MOPS/HEPES-Na pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.37→83.343 Å / Num. obs: 24725 / % possible obs: 99.94 % / Redundancy: 23 % / CC1/2: 0.97 / Net I/σ(I): 25
Reflection shellResolution: 2.37→2.45 Å / Num. unique obs: 2575 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→83.343 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.18 / SU B: 18.042 / SU ML: 0.353 / Average fsc free: 0.7125 / Average fsc work: 0.7252 / Cross valid method: FREE R-VALUE / ESU R: 0.497 / ESU R Free: 0.265
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2454 1242 5.023 %
Rwork0.2025 23483 -
all0.205 --
obs-24725 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 78.043 Å2
Baniso -1Baniso -2Baniso -3
1-13.654 Å20 Å23.214 Å2
2---10.043 Å20 Å2
3----4.674 Å2
Refinement stepCycle: LAST / Resolution: 2.37→83.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 0 161 4713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0134649
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174357
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.6576290
X-RAY DIFFRACTIONr_angle_other_deg1.0651.57110115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82822.439246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03715790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6991532
X-RAY DIFFRACTIONr_chiral_restr0.0250.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02942
X-RAY DIFFRACTIONr_nbd_refined0.2060.21233
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2420.24188
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22300
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.10.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.228
X-RAY DIFFRACTIONr_nbd_other0.2820.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0990.22
X-RAY DIFFRACTIONr_mcbond_it5.3028.1312306
X-RAY DIFFRACTIONr_mcbond_other5.3028.1292305
X-RAY DIFFRACTIONr_mcangle_it7.89212.1872879
X-RAY DIFFRACTIONr_mcangle_other7.89112.1892880
X-RAY DIFFRACTIONr_scbond_it5.5728.722343
X-RAY DIFFRACTIONr_scbond_other5.5518.7172341
X-RAY DIFFRACTIONr_scangle_it8.65612.8463411
X-RAY DIFFRACTIONr_scangle_other8.65512.8473411
X-RAY DIFFRACTIONr_lrange_it12.15799.7715372
X-RAY DIFFRACTIONr_lrange_other12.1699.7765361
X-RAY DIFFRACTIONr_ncsr_local_group_10.1650.058675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.37-2.4320.309930.35516840.35317770.3840.3270.306
2.432-2.4980.351890.35617530.35518420.3850.3830.302
2.498-2.570.315580.33216210.33116790.510.4880.282
2.57-2.650.347830.32416280.32517110.5190.5220.275
2.65-2.7360.34860.30315090.30515950.4970.5710.263
2.736-2.8320.301910.2915040.29115950.5970.6210.254
2.832-2.9390.384700.25414460.25915160.6020.7210.22
2.939-3.0590.311740.25113770.25414510.7570.8050.223
3.059-3.1950.278810.21913570.22314380.8390.8720.196
3.195-3.350.239970.20812290.2113260.8880.8990.19
3.35-3.5310.26490.20312240.20512730.9090.9210.19
3.531-3.7450.216600.18211640.18412240.9320.940.173
3.745-4.0030.227610.15710640.16111250.9430.9530.148
4.003-4.3230.229540.1549930.15710470.9280.9580.148
4.323-4.7340.205500.1439260.1469760.9470.960.137
4.734-5.2910.189380.1588420.1598800.9580.9540.153
5.291-6.1050.228380.1927520.1947900.9290.9430.187
6.105-7.4680.276310.2026540.2056850.9150.9410.199
7.468-10.5190.142310.1394730.1395040.970.9730.14
10.519-83.3430.25280.2032830.2042910.9330.9440.197

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