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- PDB-2fif: Crystal Structure of a Bovine Rabex-5 fragment complexed with ubi... -

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Basic information

Entry
Database: PDB / ID: 2fif
TitleCrystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin
Components
  • Rab5 GDP/GTP exchange factor
  • Ubiquitin
KeywordsPROTEIN TURNOVER/ENDOCYTOSIS / zinc finger / helix / PROTEIN TURNOVER-ENDOCYTOSIS COMPLEX
Function / homology
Function and homology information


: / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 ...: / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab5 GDP/GTP exchange factor / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsLee, S. / Hurley, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5
Authors: Lee, S. / Tsai, Y.C. / Mattera, R. / Smith, W.J. / Kostelansky, M.S. / Weissman, A.M. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionDec 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Remark 300Biomolecule: 1 The biological assembly is rabex-5 complexed with two ubiquitin molecules. This ...Biomolecule: 1 The biological assembly is rabex-5 complexed with two ubiquitin molecules. This correspondis to chain B with chains A and E in the asymmetric unit.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Rab5 GDP/GTP exchange factor
C: Ubiquitin
D: Rab5 GDP/GTP exchange factor
E: Ubiquitin
F: Rab5 GDP/GTP exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,39510
Polymers50,1026
Non-polymers2924
Water34219
1
A: Ubiquitin
B: Rab5 GDP/GTP exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8624
Polymers16,7012
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-16 kcal/mol
Surface area8820 Å2
MethodPISA
2
C: Ubiquitin
D: Rab5 GDP/GTP exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7663
Polymers16,7012
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin
F: Rab5 GDP/GTP exchange factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7663
Polymers16,7012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.200, 44.420, 69.170
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is rabex-5 complexed with two ubiquitin molecules. This would correspond to chain B with chains A and E in the asymmetric unit.

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62990, UniProt: P0CH28*PLUS
#2: Protein Rab5 GDP/GTP exchange factor / Rabex-5


Mass: 8123.975 Da / Num. of mol.: 3
Fragment: A20 zinc finger and inverted ubiquitin interacting motif domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RABGEF1, RABEX5 / Plasmid: parallel GST2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O18973
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.49→90.91 Å / Num. all: 19257 / Num. obs: 19257 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.49→2.59 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2FID

2fid


Resolution: 2.49→90.91 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.649 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26347 985 5.1 %RANDOM
Rwork0.22821 ---
all0.23003 18271 --
obs0.23003 18271 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.197 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.21 Å2
2--0.9 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.49→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 8 19 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223262
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.9654382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83925.207169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52715636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6821521
X-RAY DIFFRACTIONr_chiral_restr0.070.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022451
X-RAY DIFFRACTIONr_nbd_refined0.1780.21315
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.215
X-RAY DIFFRACTIONr_mcbond_it0.2451.52011
X-RAY DIFFRACTIONr_mcangle_it0.42623124
X-RAY DIFFRACTIONr_scbond_it0.68831432
X-RAY DIFFRACTIONr_scangle_it1.0774.51258
LS refinement shellResolution: 2.492→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 61 -
Rwork0.321 1137 -
obs--85.09 %
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)
13.0871.6437-0.15836.3617-2.06026.54660.1104-0.29680.10970.4605-0.02750.0607-0.16760.1288-0.0829-0.2448-0.0014-0.0039-0.3859-0.0354-0.266143.64096.354410.4229
215.6228-2.4764-7.53497.0593-1.2888.5124-0.0292-0.23590.8121-0.17070.46350.8744-0.2533-0.752-0.4343-0.1540.04610.01820.04220.04050.0239117.1598-3.232815.9929
316.1285-0.63021.69855.5651-0.56067.2807-0.33710.49140.9778-0.5195-0.1505-0.2088-0.60521.58210.4876-0.0432-0.0929-0.15630.42720.11440.0214176.7764-16.88920.192
415.47571.42137.860118.88964.758420.85440.5584-1.1516-0.61611.0565-0.2998-0.41591.0063-0.4503-0.2587-0.14540.0117-0.1849-0.035-0.0137-0.0561158.0977-23.246218.7878
516.0741-8.9729-7.121214.64951.358423.86760.42791.9552-0.6855-0.7162-0.89460.33951.1757-0.81730.46670.13220.08930.0012-0.0067-0.1199-0.2141124.7377-25.233537.9852
615.99560.3561-2.620718.3449-6.61737.1637-1.25191.6056-2.104-0.05771.2807-0.52890.91710.4716-0.02880.1609-0.05830.36130.7328-0.46710.4996160.1725-37.351538.5014
717.8673-14.71968.802418.0771-9.39348.5511-0.1858-0.57450.54820.1340.34940.0844-0.1105-0.5258-0.1636-0.2649-0.05760.0098-0.4077-0.035-0.2158139.5021-3.83153.3567
86.5677-4.5819.417813.4252-22.160764.5651-0.33750.2018-0.2116-0.77060.0530.39960.8045-0.37950.28450.0429-0.00030.08310.00570.04090.0013124.7656-13.028111.3079
920.85955.0953-19.21865.1876-3.363225.5132-0.3138-0.0267-0.6368-0.4569-0.4226-0.18770.19021.42550.7364-0.09910.2099-0.04470.62280.05350.216181.4065-29.398322.5921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 731 - 73
2X-RAY DIFFRACTION2CC1 - 731 - 73
3X-RAY DIFFRACTION3EE1 - 731 - 73
4X-RAY DIFFRACTION4BB15 - 3712 - 34
5X-RAY DIFFRACTION5DD16 - 3713 - 34
6X-RAY DIFFRACTION6FF17 - 3714 - 34
7X-RAY DIFFRACTION7BB38 - 7335 - 70
8X-RAY DIFFRACTION8DD38 - 7335 - 70
9X-RAY DIFFRACTION9FF38 - 7235 - 69

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