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- PDB-4cc4: Complex of InlC of Listeria monocytogenes and human Tuba C-termin... -

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Basic information

Entry
Database: PDB / ID: 4cc4
TitleComplex of InlC of Listeria monocytogenes and human Tuba C-terminal SH3 domain
Components
  • (INLC PROTEIN) x 2
  • DYNAMIN-BINDING PROTEIN
KeywordsCELL INVASION / BACTERIAL INFECTION / PATHOGENESIS / LISTERIAL CELL-CELL SPREAD / VIRULENCE FACTOR / PROTEIN-PROTEIN INTERACTIONS / LEUCINE-RICH REPEAT / SRC HOMOLOGY 3 DOMAIN / DISRUPTION OF CORTICAL TENSION / CELL MEMBRANE PROTRUSIONS
Function / homology
Function and homology information


Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / host cell cytoplasm / cytoskeleton ...Golgi stack / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / guanyl-nucleotide exchange factor activity / cell-cell junction / presynapse / regulation of cell shape / host cell cytoplasm / cytoskeleton / intracellular signal transduction / synapse / Golgi apparatus / extracellular region / cytoplasm / cytosol
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / BAR domain ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / Immunoglobulin-like - #1220 / BAR domain / BAR domain profile. / BAR / BAR domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / AH/BAR domain superfamily / Variant SH3 domain / Variant SH3 domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Alpha-Beta Horseshoe / SH3 Domains / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / SH3 domain / Leucine-rich repeat domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin E-set / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Internalin C / Dynamin-binding protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES EGD-E (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPolle, L. / Rigano, L. / Julian, R. / Ireton, K. / Schubert, W.-D.
CitationJournal: Structure / Year: 2014
Title: Structural Details of Human Tuba Recruitment by Inlc of Listeria Monocytogenes Elucidate Bacterial Cell-Cell Spreading.
Authors: Polle, L. / Rigano, L.A. / Julian, R. / Ireton, K. / Schubert, W.
History
DepositionOct 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 2.0Jul 5, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _diffrn_source.type / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_close_contact.label_alt_id_1 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.label_alt_id_1 / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.id / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INLC PROTEIN
B: DYNAMIN-BINDING PROTEIN
C: INLC PROTEIN
D: DYNAMIN-BINDING PROTEIN
E: INLC PROTEIN
F: DYNAMIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,90022
Polymers112,4916
Non-polymers1,41016
Water5,044280
1
A: INLC PROTEIN
B: DYNAMIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7225
Polymers37,5022
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-1.6 kcal/mol
Surface area20270 Å2
MethodPQS
2
C: INLC PROTEIN
D: DYNAMIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,32310
Polymers37,4862
Non-polymers8378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-3.3 kcal/mol
Surface area19550 Å2
MethodPQS
3
E: INLC PROTEIN
F: DYNAMIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8557
Polymers37,5022
Non-polymers3535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-5.5 kcal/mol
Surface area19520 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.702, 101.750, 126.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules AEBDFC

#1: Protein INLC PROTEIN / INLC / INTERNALIN / INTERNALIN B / INTERNALIN C


Mass: 29718.535 Da / Num. of mol.: 2 / Fragment: INTERNALIN DOMAIN, RESIDUES 35-297 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES EGD-E (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P71451
#2: Protein DYNAMIN-BINDING PROTEIN / TUBA SH3-6 / SCAFFOLD PROTEIN TUBA


Mass: 7783.694 Da / Num. of mol.: 3 / Fragment: C-TERMINAL SH3 DOMAIN OF TUBA, RESIDUES 1513-1577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q6XZF7
#3: Protein INLC PROTEIN / INLC / INTERNALIN / INTERNALIN B / INTERNALIN C


Mass: 29702.535 Da / Num. of mol.: 1 / Fragment: INTERNALIN DOMAIN, RESIDUES 35-297 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES EGD-E (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P71451

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Non-polymers , 6 types, 296 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details3 N-TERMINAL AMINO ACIDS DERIVE FROM FUSION PROTEIN CLEAVAGE SITE N-TERMINAL TWO RESIDUES GP DERIVE ...3 N-TERMINAL AMINO ACIDS DERIVE FROM FUSION PROTEIN CLEAVAGE SITE N-TERMINAL TWO RESIDUES GP DERIVE FROM FUSION PROTEIN CLEAVAGE

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.8 M NA2HPO4, 0.8 M K2HPO4, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 3, 2011 / Details: OSMIC VARIMAX
RadiationMonochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 36275 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1XEU, 1ZUU

1xeu

1zuu


Resolution: 2.6→14.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 23.93 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 1.892 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.N U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26187 1806 5 %RANDOM
Rwork0.19584 ---
obs0.19914 34331 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.137 Å2
Baniso -1Baniso -2Baniso -3
1--4.46 Å20 Å20 Å2
2--3.96 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7844 0 75 280 8199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028315
X-RAY DIFFRACTIONr_bond_other_d0.0020.028046
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.97411318
X-RAY DIFFRACTIONr_angle_other_deg0.843318590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08951060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.20725.775400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.591151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0171537
X-RAY DIFFRACTIONr_chiral_restr0.0930.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021865
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 150 -
Rwork0.296 2488 -
obs--98.14 %
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)
13.18472.01081.48714.01652.34922.6169-0.064-0.2952-0.23440.1198-0.08680.1740.1439-0.04070.15080.44940.0420.0180.04550.06670.146120.56614.08230.883
23.57611.58422.93256.71683.05076.6085-0.15470.12170.2105-0.4706-0.02090.2395-0.60350.02390.17560.67440.0347-0.08590.00820.01160.120516.14225.8912.808
33.2873-0.5345-2.4770.8426-0.12975.29950.01620.36370.1140.05190.0770.2488-0.0146-0.8645-0.09320.38990.00680.00610.15750.06940.222331.74-8.94442.015
43.32310.0176-2.5814.191-3.20348.1262-0.1653-0.3724-0.22390.4618-0.2387-0.3569-0.07570.64050.4040.49670.0385-0.02150.06820.05850.176446.081-14.65158.295
53.86832.33482.50492.99072.20694.1607-0.15450.40080.4046-0.0410.0312-0.2902-0.19930.32690.12330.4959-0.02240.02710.08830.14620.3234-15.5887.72735.147
67.96442.71172.74073.4517-0.03341.3410.4894-1.1270.19660.7727-0.47860.1097-0.0702-0.3055-0.01080.7071-0.13890.03810.292-0.04390.2839-23.434-0.17353.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 297
2X-RAY DIFFRACTION2B1511 - 1578
3X-RAY DIFFRACTION3C34 - 298
4X-RAY DIFFRACTION4D1515 - 1577
5X-RAY DIFFRACTION5E35 - 297
6X-RAY DIFFRACTION6F1511 - 1577

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