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

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Basic information

Entry
Database: PDB / ID: 2hfe
TitleRb+ complex of a K channel with an amide to ester substitution in the selectivity filter
Components
  • FAB Heavy ChainFragment antigen-binding
  • FAB Light ChainFragment antigen-binding
  • KcsA channel
KeywordsMEMBRANE PROTEIN / channel / semi-synthetic / ester
Function / homology
Function and homology information


monoatomic ion transmembrane transport / 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 / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...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 / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(2S)-2-(BUTYRYLOXY)-3-HYDROXYPROPYL NONANOATE / RUBIDIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 23, 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: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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_asym_id / _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.ptnr1_symmetry / _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_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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_biol / 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_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _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.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THERE WERE NO UNP REFERENCE SEQUENCES AVAILABLE FOR THE PROTEINS.
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.

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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)58,2459
Polymers57,5153
Non-polymers7306
Water1,802100
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)232,98136
Polymers230,06212
Non-polymers2,91924
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
Buried area34840 Å2
ΔGint-212 kcal/mol
Surface area87510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.142, 156.142, 75.794
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-

RB

21C-202-

RB

31C-203-

RB

41C-204-

RB

51C-205-

RB

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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 KcsA peptide was synthesised by the expressed protein ligation reaction between a recombinant peptide thioester and a synthetic peptide consisting of an N-terminal cysteine
Source: (synth.) synthetic construct (others) / References: UniProt: P0A333*PLUS

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Antibody , 2 types, 2 molecules AB

#1: Antibody FAB Heavy Chain / Fragment antigen-binding


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma cell line / Production host: Escherichia coli (E. coli)
#2: Antibody FAB Light Chain / Fragment antigen-binding


Mass: 23321.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma cell line / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 106 molecules

#4: Chemical
ChemComp-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Rb / References: UniProt: P0A333*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 / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 4.02 Å3/Da / Density % sol: 69.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20-25% PEG400, 50 mM Magnesium Acetate, 0.3M RbCl, 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: 2.25→100 Å / Num. obs: 43036 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 21.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.57 / Num. unique all: 4327 / Rsym value: 0.462 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→26.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2354853 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2155 5 %RANDOM
Rwork0.232 ---
all-43036 --
obs-42966 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.078 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.15 Å20 Å20 Å2
2--8.15 Å20 Å2
3----16.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→26.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 30 100 4172
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 364 5.1 %
Rwork0.298 6799 -
obs-7163 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_mod.top
X-RAY DIFFRACTION2lipid2.paramlipid_mod.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4Rb.paramrb_xplor_top.txt

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