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- PDB-5wy2: Human Snx5 PX domain in complex with Chlamydia IncE C terminus -

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Basic information

Entry
Database: PDB / ID: 5wy2
TitleHuman Snx5 PX domain in complex with Chlamydia IncE C terminus
Components
  • IncE
  • Sorting nexin-5
KeywordsTRANSPORT PROTEIN/UNKNOWN FUNCTION / Complex / IncE / PX domain / Snx5 / TRANSPORT PROTEIN-UNKNOWN FUNCTION complex
Function / homology
Function and homology information


retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding ...retromer, tubulation complex / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / retromer complex / retrograde transport, endosome to Golgi / phagocytic cup / Golgi Associated Vesicle Biogenesis / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / membrane / cytosol
Similarity search - Function
Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. ...Inclusion membrane protein E / Inclusion membrane protein E / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IncE / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Chlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSun, Q. / Yong, X. / Jia, D.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC81502629 China
CitationJournal: Signal Transduct Target Ther / Year: 2017
Title: Structural and functional insights into sorting nexin 5/6 interaction with bacterial effector IncE.
Authors: Sun, Q. / Yong, X. / Sun, X. / Yang, F. / Dai, Z. / Gong, Y. / Zhou, L. / Zhang, X. / Niu, D. / Dai, L. / Liu, J.J. / Jia, D.
History
DepositionJan 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.page_first ..._citation.country / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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: Sorting nexin-5
B: IncE
C: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)41,6114
Polymers41,6114
Non-polymers00
Water4,414245
1
A: Sorting nexin-5
B: IncE


Theoretical massNumber of molelcules
Total (without water)20,8052
Polymers20,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area9520 Å2
MethodPISA
2
C: Sorting nexin-5
D: IncE


Theoretical massNumber of molelcules
Total (without water)20,8052
Polymers20,8052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.443, 43.711, 60.070
Angle α, β, γ (deg.)94.79, 99.81, 100.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA28 - 17611 - 159
21ASPASPARGARGCC28 - 17611 - 159
12GLYGLYTHRTHRBB111 - 1311 - 21
22GLYGLYTHRTHRDD111 - 1311 - 21

NCS ensembles :
ID
1
2

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Components

#1: Protein Sorting nexin-5 /


Mass: 18626.916 Da / Num. of mol.: 2 / Fragment: UNP residues 20-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3
#2: Protein/peptide IncE


Mass: 2178.486 Da / Num. of mol.: 2 / Fragment: UNP residues 111-131 / Source method: obtained synthetically / Source: (synth.) Chlamydia trachomatis (bacteria) / References: UniProt: B7SCI5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate pH 4.6, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50.01 Å / Num. obs: 27655 / % possible obs: 96.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.069 / Rrim(I) all: 0.096 / Χ2: 1.062 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.9-1.930.85913780.3660.8590.99595.8
1.93-1.970.650.4860.6390.96296.30.911
1.97-2.010.5440.5290.5341.05396.50.762
2.01-2.050.4560.6450.4491.05396.70.64
2.05-2.090.3750.7260.3691.03596.40.526
2.09-2.140.3510.7530.3451.14296.50.492
2.14-2.190.2830.8250.2781.13196.40.397
2.19-2.250.2490.8270.2451.17796.40.349
2.25-2.320.2030.8850.21.04970.285
2.32-2.390.1790.90.1761.13397.10.251
2.39-2.480.1430.9470.1411.05596.90.201
2.48-2.580.1250.9540.1231.19497.10.176
2.58-2.70.0950.9740.0931.00696.20.133
2.7-2.840.0790.980.0781.094970.111
2.84-3.020.0660.9880.0651.01396.80.093
3.02-3.250.0570.9850.0561.0196.60.08
3.25-3.580.0480.990.0471.07297.10.067
3.58-4.090.0440.990.0420.95295.30.061
4.09-5.160.0420.9890.0411.05195.20.059
5.16-500.0490.9870.0491.065980.069

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HPC

3hpc


Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.376 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22274 1347 4.9 %RANDOM
Rwork0.18736 ---
obs0.18912 26308 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.342 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.24 Å2-0.22 Å2
2---0.02 Å20.31 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 0 245 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192715
X-RAY DIFFRACTIONr_bond_other_d0.0020.022513
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.963671
X-RAY DIFFRACTIONr_angle_other_deg0.9535862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96624.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6421514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6642.6141311
X-RAY DIFFRACTIONr_mcbond_other1.6642.6131310
X-RAY DIFFRACTIONr_mcangle_it2.8643.8941630
X-RAY DIFFRACTIONr_mcangle_other2.8633.8961631
X-RAY DIFFRACTIONr_scbond_it1.4882.7341404
X-RAY DIFFRACTIONr_scbond_other1.4872.7351405
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4874.0032042
X-RAY DIFFRACTIONr_long_range_B_refined5.2430.8113080
X-RAY DIFFRACTIONr_long_range_B_other5.23830.8073079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88260.09
12C88260.09
21B9340.17
22D9340.17
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 96 -
Rwork0.289 1807 -
obs--91.53 %
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)
13.84610.5638-1.50673.90390.71864.33990.0331-0.3617-0.17970.5305-0.10630.30210.0536-0.21610.07320.0789-0.00790.06410.0710.00670.108-0.95990.03010.1713
29.27640.536-1.12822.55020.18020.5955-0.017-0.16980.16780.0592-0.0286-0.04990.02870.00510.04560.1724-0.0040.01010.17190.02080.0731-3.42934.456114.8108
33.1934-0.22651.78463.40820.83795.1149-0.05730.27170.0674-0.6062-0.1410.2157-0.1045-0.17820.19830.1649-0.00520.04280.0542-0.03250.146416.5625-17.4593-26.8872
414.5931-1.51472.53345.3889-0.41593.20040.02010.6571-0.4801-0.0803-0.019-0.1376-0.04740.0868-0.00110.28770.01870.01110.2209-0.02150.079815.1853-22.2012-39.9294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 176
2X-RAY DIFFRACTION1A201 - 320
3X-RAY DIFFRACTION2B111 - 131
4X-RAY DIFFRACTION2B201 - 203
5X-RAY DIFFRACTION3C28 - 176
6X-RAY DIFFRACTION3C201 - 317
7X-RAY DIFFRACTION4D111 - 131
8X-RAY DIFFRACTION4D201 - 205

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