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- PDB-3b76: Crystal structure of the third PDZ domain of human ligand-of-numb... -

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Basic information

Entry
Database: PDB / ID: 3b76
TitleCrystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor
ComponentsE3 ubiquitin-protein ligase LNX
KeywordsLIGASE / PDZ / bound ligand / Structural Genomics / Structural Genomics Consortium / SGC / Metal-binding / Ubl conjugation pathway / Zinc-finger / UNKNOWN FUNCTION
Function / homology
Function and homology information


synapse maturation / hippocampal mossy fiber to CA3 synapse / PDZ domain binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / zinc ion binding ...synapse maturation / hippocampal mossy fiber to CA3 synapse / PDZ domain binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / postsynapse / protein ubiquitination / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PDZ domain / Ring finger / PDZ domain profile. ...: / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PDZ domain / Ring finger / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase LNX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsUgochukwu, E. / Burgess-Brown, N. / Berridge, G. / Elkins, J. / Bunkoczi, G. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. ...Ugochukwu, E. / Burgess-Brown, N. / Berridge, G. / Elkins, J. / Bunkoczi, G. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Gileadi, O. / von Delft, F. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor.
Authors: Ugochukwu, E. / Burgess-Brown, N. / Berridge, G. / Elkins, J. / Bunkoczi, G. / Pike, A.C.W. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Gileadi, O. / von Delft, F. / Doyle, D.
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
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_ncs_dom_lim / 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_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_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.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.end_auth_comp_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 999 SEQUENCE This is a C-terminal peptide from the coxsackievirus and adenovirus receptor.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase LNX
B: E3 ubiquitin-protein ligase LNX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7965
Polymers25,6492
Non-polymers1473
Water2,234124
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.782, 58.449, 73.741
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
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 402 - 502 / Label seq-ID: 18 - 118

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein E3 ubiquitin-protein ligase LNX / Numb-binding protein 1 / Ligand of Numb-protein X 1


Mass: 12824.500 Da / Num. of mol.: 2 / Fragment: Third PDZ domain: Residues 504-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX1, LNX / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-Rosetta
References: UniProt: Q8TBB1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.53M Potassium phosphate, 0.27M Sodium phosphate, 1% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99975 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99975 Å / Relative weight: 1
ReflectionResolution: 1.75→33.71 Å / Num. all: 22359 / Num. obs: 22359 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 16
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.9 / Num. unique all: 23287 / Rsym value: 0.844 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L

2aww

2byg

2awx

2awu

2g2l


Resolution: 1.75→33.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.124 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20529 1144 5.1 %RANDOM
Rwork0.175 ---
all0.17657 21214 --
obs0.17657 21214 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 9 124 1646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221546
X-RAY DIFFRACTIONr_bond_other_d0.0020.021029
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9862088
X-RAY DIFFRACTIONr_angle_other_deg1.91332542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77224.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64815279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.689159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
X-RAY DIFFRACTIONr_nbd_refined0.1880.2240
X-RAY DIFFRACTIONr_nbd_other0.1960.21036
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2730
X-RAY DIFFRACTIONr_nbtor_other0.0880.2857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.214
X-RAY DIFFRACTIONr_mcbond_it3.71151001
X-RAY DIFFRACTIONr_mcbond_other1.5665418
X-RAY DIFFRACTIONr_mcangle_it5.19471618
X-RAY DIFFRACTIONr_scbond_it7.1649559
X-RAY DIFFRACTIONr_scangle_it10.0211470
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A592medium positional0.70.5
2B633loose positional1.155
1A592medium thermal2.972
2B633loose thermal3.4410
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 67 -
Rwork0.224 1529 -
obs--99.94 %
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)
10.742-0.0921-0.20551.5999-0.0270.6760.03580.0660.018-0.18870.016-0.05560.00230.064-0.0519-0.01180.00610.0136-0.0431-0.0007-0.04596.61613.817914.0596
21.3140.3064-0.94890.48960.17071.8422-0.0102-0.0431-0.0461-0.0479-0.03550.04-0.0581-0.01970.0457-0.03860.0041-0.0075-0.0481-0.0162-0.0327-5.6228.596329.6785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA402 - 50218 - 118
2X-RAY DIFFRACTION2BB401 - 50217 - 118

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