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- PDB-4ux3: cohesin Smc3-HD:Scc1-N complex from yeast -

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Basic information

Entry
Database: PDB / ID: 4ux3
Titlecohesin Smc3-HD:Scc1-N complex from yeast
Components
  • MITOTIC CHROMOSOME DETERMINANT-RELATED PROTEIN
  • STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3
KeywordsPROTEIN BINDING / COHESIN / MITOSIS / CHROMOSOME SEGREGATION / KLEISIN / SMC
Function / homology
Function and homology information


Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion ...Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic cohesin complex / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / synaptonemal complex assembly / SUMOylation of DNA damage response and repair proteins / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / reciprocal meiotic recombination / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / double-strand break repair / double-stranded DNA binding / cell division / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus
Similarity search - Function
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily ...Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Mitotic chromosome determinant-related protein / Structural maintenance of chromosomes protein 3 / Sister chromatid cohesion protein 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGligoris, T.G. / Nasmyth, K. / Lowe, J.
CitationJournal: Science / Year: 2014
Title: Closing the Cohesin Ring: Structure and Function of its Smc3-Kleisin Interface.
Authors: Gligoris, T.G. / Scheinost, J.C. / Burmann, F. / Petela, N. / Chan, K. / Uluocak, P. / Beckouet, F. / Gruber, S. / Nasmyth, K. / Lowe, J.
History
DepositionAug 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3
B: MITOTIC CHROMOSOME DETERMINANT-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1094
Polymers75,5612
Non-polymers5482
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-45.5 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.151, 94.801, 284.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 / DA-BOX PROTEIN SMC3 / SMC3


Mass: 62072.840 Da / Num. of mol.: 1
Fragment: HEAD DOMAIN WITH COILED COIL SEGMENT, RESIDUES 2-261 AND RESIDUES 970-1230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P47037
#2: Protein MITOTIC CHROMOSOME DETERMINANT-RELATED PROTEIN / SCC1


Mass: 13488.373 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A6ZXW3, UniProt: Q12158*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 60 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97957
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 15350 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 26.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XEX

1xex


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 106.2 / SU ML: 0.781 / Cross valid method: THROUGHOUT / ESU R Free: 0.585
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.32861 765 5 %RANDOM
Rwork0.27382 ---
obs0.27663 14583 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 182.117 Å2
Baniso -1Baniso -2Baniso -3
1--8.86 Å20 Å20 Å2
2--23.84 Å20 Å2
3----14.98 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 32 0 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9735555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5015501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08525.196204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51615827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3621528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023016
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.39710.5262022
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.50815.7772517
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.12911.5622114
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: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 41 -
Rwork0.409 1060 -
obs--99.91 %
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)
17.16242.4270.38531.8189-1.29443.2059-0.07340.0049-1.2524-0.03820.1631-0.12580.5731-0.6353-0.08981.0418-0.20130.18190.1645-0.09381.1849-154.4551-69.5404608.1413
20.1766-0.19730.27030.9959-2.55517.11630.0276-0.16690.02590.24840.11830.0361-0.4397-0.0788-0.1460.8131-0.0317-0.02450.62050.05270.602-142.4483-70.9251675.5709
32.31451.77-5.85482.0942-6.340721.4471-0.0312-0.3778-0.22350.1124-0.2384-0.09420.00870.68440.26960.75980.0377-0.04170.59580.00250.8253-136.3445-66.17646.1177
43.78870.58970.75442.5546-0.68372.3376-0.07630.9292-0.6485-0.35770.0049-0.21170.1090.56760.07140.90070.06270.1510.5233-0.18080.6918-137.6146-56.9588600.7049
523.3344.7911-4.309324.049214.070410.496-0.1283-0.685-0.8493.0152-0.94221.28651.9696-0.40691.07041.2205-0.1727-0.02421.46070.17650.7939-146.6703-61.1634582.8941
64.2479-1.4248-0.87340.48020.29840.2234-0.11170.7291-1.53810.0607-0.22380.48840.08880.05920.33551.5971-0.02980.01071.1992-0.11491.149-142.9199-76.8798642.0604
73.86350.7217-3.29672.9994-1.513413.0811-0.39920.5027-0.5519-0.4655-0.0441-0.43980.63970.10570.44330.835-0.0504-0.08870.43860.06490.8262-140.639-70.8218645.0033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 156
2X-RAY DIFFRACTION2A157 - 988
3X-RAY DIFFRACTION3A989 - 1062
4X-RAY DIFFRACTION4A1063 - 1213
5X-RAY DIFFRACTION5A1214 - 1222
6X-RAY DIFFRACTION6B25 - 43
7X-RAY DIFFRACTION7B44 - 102

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