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- PDB-7jya: Crystal structure of E3 ligase in complex with peptide -

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Basic information

Entry
Database: PDB / ID: 7jya
TitleCrystal structure of E3 ligase in complex with peptide
Components
  • ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG
  • Protein fem-1 homolog C
KeywordsLIGASE / UPS / ubiquitin / E3 ligase / protein degradation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


host cell nucleolus / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Cul2-RING ubiquitin ligase complex / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion ...host cell nucleolus / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Cul2-RING ubiquitin ligase complex / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral process / Binding and entry of HIV virion / ubiquitin ligase complex / mRNA transport / ubiquitin-like ligase-substrate adaptor activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / protein ubiquitination / DNA-binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Protein Rev / Protein fem-1 homolog C
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.46 Å
AuthorsYan, X. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J.R. / Dong, C. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Molecular basis for ubiquitin ligase CRL2 FEM1C -mediated recognition of C-degron.
Authors: Yan, X. / Wang, X. / Li, Y. / Zhou, M. / Li, Y. / Song, L. / Mi, W. / Min, J. / Dong, C.
History
DepositionAug 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein fem-1 homolog C
B: Protein fem-1 homolog C
C: Protein fem-1 homolog C
D: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG
E: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG
F: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG


Theoretical massNumber of molelcules
Total (without water)128,30411
Polymers128,3046
Non-polymers05
Water34219
1
A: Protein fem-1 homolog C


Theoretical massNumber of molelcules
Total (without water)41,0923
Polymers41,0921
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein fem-1 homolog C


Theoretical massNumber of molelcules
Total (without water)41,0924
Polymers41,0921
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein fem-1 homolog C


Theoretical massNumber of molelcules
Total (without water)41,0921
Polymers41,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG


Theoretical massNumber of molelcules
Total (without water)1,6761
Polymers1,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG


Theoretical massNumber of molelcules
Total (without water)1,6761
Polymers1,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG


  • defined by author&software
  • 1.68 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,6761
Polymers1,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.133, 100.133, 287.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALABB310 - 313310 - 313
21GLYGLYALAALAAA310 - 313310 - 313
12GLYGLYALAALACC310 - 313310 - 313
22GLYGLYALAALAAA310 - 313310 - 313
13THRTHRILEILEAA281 - 283281 - 283
23THRTHRILEILEBB281 - 283281 - 283

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.80648, 0.556626, -0.199393), (0.373774, -0.218662, 0.901377), (0.45813, -0.80147, -0.384399)-25.87109, 81.556839, -44.544449

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Components

#1: Protein Protein fem-1 homolog C / FEM1c / FEM1-gamma


Mass: 41092.117 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEM1C, KIAA1785 / Plasmid: pET15-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V3R / References: UniProt: Q96JP0
#2: Protein/peptide ASN-ARG-ARG-ARG-ARG-TRP-ARG-GLU-ARG-GLN-ARG


Mass: 1675.927 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04618*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.2 % / Mosaicity: 0.275 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 16% Jeffamine M-600 pH 7.0 and 0.1 M HEPES 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 53959 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 0.866 / Net I/σ(I): 9.1 / Num. measured all: 366983
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.46-2.56.70.9726920.8520.3971.0510.67999.9
2.5-2.556.50.81826070.8970.3410.8890.69399.8
2.55-2.66.30.73626360.8760.3110.8020.69999.7
2.6-2.655.80.57926620.9230.2550.6350.70499.3
2.65-2.716.10.50926390.9460.2180.5560.69699.4
2.71-2.777.20.41926790.9580.1660.4520.706100
2.77-2.847.20.37126370.9660.1460.40.731100
2.84-2.927.30.2826790.9840.110.3020.734100
2.92-37.20.2226620.990.0870.2370.74100
3-3.17.10.18126960.9930.0720.1950.785100
3.1-3.2170.13726670.9940.0550.1480.82599.7
3.21-3.3470.11427150.9960.0460.1240.84299.7
3.34-3.496.80.08226480.9970.0340.0890.90499.8
3.49-3.676.60.06327160.9980.0260.0681.04199.9
3.67-3.95.90.0526850.9980.0220.0551.15698.9
3.9-4.217.10.04427110.9990.0180.0481.1899.6
4.21-4.637.50.03827430.9990.0150.0411.17299.7
4.63-5.37.40.03527620.9990.0130.0371.07199.6
5.3-6.6770.03227940.9990.0130.0350.91798.9
6.67-506.40.02529290.9980.0110.0270.96497.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MA4

5ma4


Resolution: 2.46→47.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 23.403 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.262
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1784 3.3 %RANDOM
Rwork0.2204 ---
obs0.2218 52135 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.65 Å2 / Biso mean: 66.136 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2--1.18 Å2-0 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.46→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 5 21 8474
Biso mean--55.77 52.33 -
Num. residues----1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138605
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177743
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.63611678
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57217807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46751126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21622.015397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.934151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.821553
X-RAY DIFFRACTIONr_chiral_restr0.050.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021784
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B20MEDIUM POSITIONAL0.030.5
1B23TIGHT THERMAL4.20.5
1B20MEDIUM THERMAL3.232
2C20MEDIUM POSITIONAL0.030.5
2C23TIGHT THERMAL2.420.5
2C20MEDIUM THERMAL2.112
3A15MEDIUM POSITIONAL0.030.5
3A18TIGHT THERMAL5.40.5
3A15MEDIUM THERMAL5.292
LS refinement shellResolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 129 -
Rwork0.298 3749 -
all-3878 -
obs--98.93 %
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)
12.7301-0.115-0.7830.84620.23551.39870.1654-0.16840.08280.0701-0.12680.0962-0.1738-0.0797-0.03860.0545-0.04710.02780.379-0.09850.03493.660837.5735-28.6873
20.63230.0510.20370.08670.3923.51850.15470.00420.1441-0.08460.01760.0447-0.2605-0.5566-0.17240.30080.0702-0.05970.41820.08350.14885.134347.4133-62.8247
31.40820.32530.09872.2872-0.59322.39240.198-0.0375-0.4928-0.34960.14290.3560.4755-0.2904-0.34080.17780.0288-0.18470.51920.01370.322516.948616.287-54.4378
47.4792-0.079-1.17711.61172.65964.58370.06950.50940.0039-0.13570.1212-0.1958-0.18950.1802-0.19060.27310.03420.04060.38680.04480.44874.188138.3523-33.5539
52.08522.285-2.81618.28123.948812.53420.30230.1321-0.27150.92890.1416-1.02530.4906-0.3686-0.44390.43930.0988-0.12880.6136-0.08720.39425.317943.8345-61.6739
62.3152-0.6105-4.09131.8699-0.77339.27540.075-0.01910.10590.57310.1196-0.0477-0.6816-0.1431-0.19460.4475-0.0311-0.06820.43340.02690.481312.307815.8016-47.7072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 371
2X-RAY DIFFRACTION2B2 - 371
3X-RAY DIFFRACTION3C2 - 371
4X-RAY DIFFRACTION4D15 - 24
5X-RAY DIFFRACTION5E17 - 24
6X-RAY DIFFRACTION6F19 - 24

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