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- PDB-5n74: Microtubule end binding protein complex -

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Basic information

Entry
Database: PDB / ID: 5n74
TitleMicrotubule end binding protein complex
Components
  • Karyogamy protein KAR9
  • Microtubule-associated protein RP/EB family member 1
Keywordsmicrotubule binding protein / Microtubule end binding protein complex
Function / homology
Function and homology information


mitotic spindle orientation checkpoint signaling / protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / karyogamy / establishment of spindle localization / protein localization to microtubule / nuclear migration along microtubule / mitotic spindle microtubule ...mitotic spindle orientation checkpoint signaling / protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / karyogamy / establishment of spindle localization / protein localization to microtubule / nuclear migration along microtubule / mitotic spindle microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / mating projection tip / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / spindle pole body / negative regulation of microtubule polymerization / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / spindle midzone / spindle assembly / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / positive regulation of microtubule polymerization / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / kinetochore / spindle pole / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / protein localization / cell migration / cell cortex / microtubule / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Karyogamy protein, KAR9 / Yeast cortical protein KAR9 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / Calponin homology domain ...Karyogamy protein, KAR9 / Yeast cortical protein KAR9 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 1 / Karyogamy protein KAR9 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKumar, A. / Steinmetz, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
CitationJournal: Structure / Year: 2017
Title: Short Linear Sequence Motif LxxPTPh Targets Diverse Proteins to Growing Microtubule Ends.
Authors: Kumar, A. / Manatschal, C. / Rai, A. / Grigoriev, I. / Degen, M.S. / Jaussi, R. / Kretzschmar, I. / Prota, A.E. / Volkmer, R. / Kammerer, R.A. / Akhmanova, A. / Steinmetz, M.O.
History
DepositionFeb 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 1
C: Microtubule-associated protein RP/EB family member 1
D: Microtubule-associated protein RP/EB family member 1
E: Microtubule-associated protein RP/EB family member 1
F: Microtubule-associated protein RP/EB family member 1
G: Microtubule-associated protein RP/EB family member 1
H: Microtubule-associated protein RP/EB family member 1
I: Karyogamy protein KAR9
J: Karyogamy protein KAR9
K: Karyogamy protein KAR9
L: Karyogamy protein KAR9
M: Karyogamy protein KAR9
N: Karyogamy protein KAR9
O: Karyogamy protein KAR9
P: Karyogamy protein KAR9


Theoretical massNumber of molelcules
Total (without water)73,70016
Polymers73,70016
Non-polymers00
Water2,054114
1
A: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 1
I: Karyogamy protein KAR9
J: Karyogamy protein KAR9


Theoretical massNumber of molelcules
Total (without water)18,4254
Polymers18,4254
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-42 kcal/mol
Surface area8010 Å2
MethodPISA
2
C: Microtubule-associated protein RP/EB family member 1
D: Microtubule-associated protein RP/EB family member 1
K: Karyogamy protein KAR9
L: Karyogamy protein KAR9


Theoretical massNumber of molelcules
Total (without water)18,4254
Polymers18,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-45 kcal/mol
Surface area8270 Å2
MethodPISA
3
E: Microtubule-associated protein RP/EB family member 1
F: Microtubule-associated protein RP/EB family member 1
M: Karyogamy protein KAR9
N: Karyogamy protein KAR9


Theoretical massNumber of molelcules
Total (without water)18,4254
Polymers18,4254
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-49 kcal/mol
Surface area8020 Å2
MethodPISA
4
G: Microtubule-associated protein RP/EB family member 1
H: Microtubule-associated protein RP/EB family member 1
O: Karyogamy protein KAR9
P: Karyogamy protein KAR9


Theoretical massNumber of molelcules
Total (without water)18,4254
Polymers18,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-42 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 183.272, 42.387
Angle α, β, γ (deg.)90.00, 112.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 6817.661 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15691, UniProt: H0XPX6*PLUS
#2: Protein/peptide
Karyogamy protein KAR9 / Cortical protein KAR9


Mass: 2394.800 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KAR9, YPL269W / Production host: Escherichia coli (E. coli) / References: UniProt: P32526
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Compound detailsChains A-H and I-P are covalently linked in the protein construct used. The absence of electron ...Chains A-H and I-P are covalently linked in the protein construct used. The absence of electron density connecting these chains do not enable us to make the exact links with full confidence.

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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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 100 mM PCTP buffer, pH 4, supplemented with 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.82 Å / Num. obs: 52463 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Rrim(I) all: 0.056 / Net I/σ(I): 2.8
Reflection shellResolution: 2.3→2.43 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.83 / Num. measured obs: 28695 / Num. unique obs: 8301 / CC1/2: 0.81 / Rpim(I) all: 0.208 / Rrim(I) all: 0.501 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJO

3gjo


Resolution: 2.3→45.82 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.278 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.266 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27059 1324 5 %RANDOM
Rwork0.23039 ---
obs0.23237 25149 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.21 Å2
2---2.25 Å20 Å2
3---1.27 Å2
Refinement stepCycle: 1 / Resolution: 2.3→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 0 114 4447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194373
X-RAY DIFFRACTIONr_bond_other_d0.0020.024385
X-RAY DIFFRACTIONr_angle_refined_deg1.1652.0085904
X-RAY DIFFRACTIONr_angle_other_deg0.924310066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3995512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05225.128234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53115839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6971541
X-RAY DIFFRACTIONr_chiral_restr0.0640.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
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_it0.6292.3042096
X-RAY DIFFRACTIONr_mcbond_other0.6292.3042095
X-RAY DIFFRACTIONr_mcangle_it1.1283.4492592
X-RAY DIFFRACTIONr_mcangle_other1.1273.4492593
X-RAY DIFFRACTIONr_scbond_it0.4972.3512277
X-RAY DIFFRACTIONr_scbond_other0.4972.3512278
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8963.5083313
X-RAY DIFFRACTIONr_long_range_B_refined3.05342.05915959
X-RAY DIFFRACTIONr_long_range_B_other2.98342.08315888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 99 -
Rwork0.303 1875 -
obs--96.34 %
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)
12.664-0.6045-0.35436.14620.68851.36860.09150.12320.1681-0.74260.09370.03060.114-0.2775-0.18530.1589-0.0053-0.05550.2033-0.03470.0825-8.943947.3958-4.6328
22.1675-2.00160.291310.3851-2.943.19440.09360.02050.12690.02550.0383-0.1972-0.27140.1271-0.13190.1654-0.0645-0.01480.221-0.04070.0706-4.853748.5648-3.0682
32.97881.6711-1.82727.8466-4.67166.283-0.09650.14160.1555-0.22790.29610.28120.123-0.3206-0.19960.0854-0.0028-0.10630.2781-0.01730.1354-21.59237.3425-19.3602
42.5266-0.78960.8574.8006-3.7156.6778-0.02480.04940.1340.2881-0.0054-0.1315-0.34260.10340.03010.0544-0.0395-0.04180.2394-0.0620.1094-17.604238.3103-17.4115
51.59490.43810.362312.00523.53453.3477-0.0617-0.02410.0769-0.0297-0.0341-0.00080.2472-0.04640.09580.0469-0.03060.05790.28760.02050.2673-9.00041.8723-31.4049
63.14420.4606-0.0398.07053.36137.3158-0.015-0.0539-0.0342-0.30960.1998-0.66780.06760.2599-0.18480.0194-0.00680.04220.22060.08270.39-5.40240.813-28.4704
71.4151-0.2180.85736.74123.19756.09120.01180.2097-0.4604-0.57-0.09570.0510.7615-0.07860.0840.342-0.11660.06890.4065-0.09510.4212-26.69341.5096-31.5883
81.9197-2.0651-0.33293.68041.5786.10540.03130.4444-0.4536-0.068-0.33820.64230.9287-0.50030.30680.2198-0.1039-0.00570.4818-0.07640.328-29.85972.3171-34.2366
90.45861.2103-0.525712.0042-1.17270.6366-0.0450.1443-0.0535-0.4272-0.0732-0.5145-0.0269-0.20410.11820.3671-0.0124-0.00790.36610.00110.35141.661449.7329-8.6958
102.5507-2.2735-1.30167.3833-1.09876.58730.4425-0.06540.6747-0.1290.07220.8319-0.47620.0765-0.51470.41670.00660.08470.47480.02520.6276-16.83352.8594-3.2119
114.00972.30790.09218.8537-5.015515.00460.0309-0.18830.37860.56020.60120.3748-1.0636-0.42-0.63210.18360.0646-0.06420.3147-0.0070.2856-28.249443.9098-20.6776
1213.24582.7658-5.64892.84642.75099.2922-0.43370.27820.0609-0.58060.17830.1708-0.51840.15420.25550.4349-0.0146-0.07740.4454-0.00270.4034-8.614736.889-21.089
134.0031-1.4349-0.94979.50354.47552.2045-0.01820.0462-0.040.4865-0.19660.45140.4061-0.07340.21470.45520.01010.00410.32020.05920.3696-4.8877-8.1704-23.9857
145.66311.12961.728414.476810.77058.45950.24680.452-0.1017-1.3663-0.0242-0.5527-0.56420.0842-0.22260.714-0.00290.19670.4120.0880.4216-9.08622.4274-41.4826
1510.00950.9849-1.519412.75611.936111.2851-0.09840.2816-0.6175-1.17270.54310.18790.04260.9219-0.44460.3839-0.051-0.11160.63680.02450.2743-32.569610.1123-40.5115
164.4153-2.9550.46672.0232-0.28390.10360.49780.1761-0.3787-0.3187-0.32560.2580.1238-0.1507-0.17220.7941-0.22010.2110.9950.03990.8698-26.5272-7.226-26.7269
170.51680.08490.05370.64380.18170.2361-0.0483-0.0591-0.10820.11120.0276-0.0991-0.0558-0.04770.02070.1885-0.0314-0.04760.4145-0.00340.3148-15.419726.9568-16.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A194 - 234
2X-RAY DIFFRACTION1A235 - 248
3X-RAY DIFFRACTION2B193 - 230
4X-RAY DIFFRACTION2B231 - 248
5X-RAY DIFFRACTION3C194 - 230
6X-RAY DIFFRACTION3C231 - 248
7X-RAY DIFFRACTION4D194 - 231
8X-RAY DIFFRACTION4D232 - 248
9X-RAY DIFFRACTION5E195 - 230
10X-RAY DIFFRACTION5E231 - 248
11X-RAY DIFFRACTION6F196 - 230
12X-RAY DIFFRACTION6F231 - 248
13X-RAY DIFFRACTION7G194 - 230
14X-RAY DIFFRACTION7G231 - 248
15X-RAY DIFFRACTION8H193 - 231
16X-RAY DIFFRACTION8H232 - 248
17X-RAY DIFFRACTION9I1 - 7
18X-RAY DIFFRACTION10J-1 - 11
19X-RAY DIFFRACTION11K-1 - 10
20X-RAY DIFFRACTION12L0 - 9
21X-RAY DIFFRACTION13M-1 - 10
22X-RAY DIFFRACTION14N-1 - 10
23X-RAY DIFFRACTION15O-4 - 7
24X-RAY DIFFRACTION16P-1 - 9
25X-RAY DIFFRACTION17S1 - 114

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