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- PDB-2hg5: Cs+ complex of a K channel with an amide to ester substitution in... -

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Basic information

Entry
Database: PDB / ID: 2hg5
TitleCs+ complex of a K channel with an amide to ester substitution in the selectivity filter
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
  • KCSA CHANNEL
KeywordsMEMBRANE PROTEIN / Channel / semi-synthetic / ester
Function / homology
Function and homology information


voltage-gated potassium channel activity / B cell differentiation / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Helix Hairpins - #70 / Potassium channel domain / Ion channel / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Helix Hairpins / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2S)-2-(BUTYRYLOXY)-3-HYDROXYPROPYL NONANOATE / : / Immunoglobulin kappa constant / pH-gated potassium channel KcsA / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsValiyaveetil, F.I. / MacKinnon, R. / Muir, T.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structural and Functional Consequences of an Amide-to-Ester Substitution in the Selectivity Filter of a Potassium Channel.
Authors: Valiyaveetil, F.I. / Sekedat, M. / Mackinnon, R. / Muir, T.W.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.0Mar 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / struct_asym / struct_biol / struct_conf / struct_conn / struct_ref / struct_ref_seq / 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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Remark 400COMPOUND CHAINS C AND D ARE LINKED AND FORM A CONTINUOUS SYNTHETIC POLYPEPTIDE. THERE IS AN ESTER ...COMPOUND CHAINS C AND D ARE LINKED AND FORM A CONTINUOUS SYNTHETIC POLYPEPTIDE. THERE IS AN ESTER BOND BETWEEN RESIDUES TYR 78 AND GOA 79 OF CHAIN C.
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THERE WERE NO UNP REFERENCE SEQUENCES AVAILABLE FOR THE PROTEINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: KCSA CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4648
Polymers57,6303
Non-polymers8345
Water52229
1
A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: KCSA CHANNEL
hetero molecules

A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: KCSA CHANNEL
hetero molecules

A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: KCSA CHANNEL
hetero molecules

A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: KCSA CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,85432
Polymers230,51812
Non-polymers3,33620
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Unit cell
Length a, b, c (Å)156.597, 156.597, 75.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-201-

CS

21C-202-

CS

31C-203-

CS

41C-204-

CS

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Components

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Protein , 1 types, 1 molecules C

#3: Protein KCSA CHANNEL


Mass: 10782.549 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS SYNTHESIZED BY THE EXPRESSED PROTEIN LIGATION REACTION BETWEEN A RECOMBINANT PEPTIDE THIOESTER AND A SYNTHETIC PEPTIDE CONSISTING OF A N-TERMINAL CYSTEINE.
Source: (synth.) synthetic construct (others) / References: UniProt: P0A334*PLUS

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Antibody , 2 types, 2 molecules AB

#1: Antibody FAB HEAVY CHAIN


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma cell line / References: UniProt: Q569B4*PLUS
#2: Antibody FAB LIGHT CHAIN


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma cell line / References: UniProt: P01837*PLUS

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Non-polymers , 3 types, 34 molecules

#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs / References: UniProt: P0A334*PLUS
#5: Chemical ChemComp-B3H / (2S)-2-(BUTYRYLOXY)-3-HYDROXYPROPYL NONANOATE


Mass: 302.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals of the KcsAester-Fab complex grown in the presence of 300 mM KCl were washed 2X in a similar solution containing 0.3M CsCl, incubated overnight in the presence of 0.3M CsCl and then ...Details: Crystals of the KcsAester-Fab complex grown in the presence of 300 mM KCl were washed 2X in a similar solution containing 0.3M CsCl, incubated overnight in the presence of 0.3M CsCl and then cryoprotected. 50 mM Magnesium acetate, PEG 400 (20-25%), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. obs: 23274 / % possible obs: 97 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Χ2: 1.657 / Net I/σ(I): 15.8
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.434 / Num. unique all: 2362 / Χ2: 1.004 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→26.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1799884.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1195 5.1 %RANDOM
Rwork0.239 ---
obs-23257 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.927 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å20 Å20 Å2
2--5.08 Å20 Å2
3----10.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.75→26.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 25 29 4110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 182 4.7 %
Rwork0.332 3715 -
obs-3897 97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_mod.top
X-RAY DIFFRACTION2lipid2.parlipid_mod.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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