[English] 日本語
Yorodumi
- PDB-4fi3: Structure of vitamin B12 transporter BtuCD-F in a nucleotide-boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fi3
TitleStructure of vitamin B12 transporter BtuCD-F in a nucleotide-bound state
Components
  • Vitamin B12 import ATP-binding protein BtuD
  • Vitamin B12 import system permease protein BtuC
  • Vitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / Vitamin B12 transport / ATP binding / Membrane
Function / homology
Function and homology information


ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein ...ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Vitamin B12 import system permease protein BtuC / Vitamin B12 import ATP-binding protein BtuD / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.466 Å
AuthorsKorkhov, V.M. / Mireku, S.A. / Locher, K.P.
CitationJournal: Nature / Year: 2012
Title: Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F.
Authors: Korkhov, V.M. / Mireku, S.A. / Locher, K.P.
History
DepositionJun 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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 / _pdbx_struct_conn_angle.value / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin B12 import system permease protein BtuC
B: Vitamin B12 import system permease protein BtuC
C: Vitamin B12 import ATP-binding protein BtuD
D: Vitamin B12 import ATP-binding protein BtuD
F: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7739
Polymers157,7125
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-99 kcal/mol
Surface area54250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.730, 211.990, 179.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A') and not ((chain 'A' and resid ' 164...
211(chain 'B') and not ((chain 'B' and resid ' 164...
112chain 'C'
212chain 'D'
113chain 'G'
213chain 'H'

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Vitamin B12 import system permease protein BtuC


Mass: 37650.617 Da / Num. of mol.: 2 / Mutation: C18S, C32S, C120S, C156S, C205S, C206S, C267S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: btuC, b1711, JW1701 / Production host: Escherichia coli (E. coli) / References: UniProt: P06609
#2: Protein Vitamin B12 import ATP-binding protein BtuD / Vitamin B12-transporting ATPase


Mass: 27086.176 Da / Num. of mol.: 2 / Mutation: C180S, E159Q, N162C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: btuD, b1709, JW1699 / Production host: Escherichia coli (E. coli) / References: UniProt: P06611, EC: 3.6.3.33
#3: Protein Vitamin B12-binding protein


Mass: 28238.096 Da / Num. of mol.: 1 / Fragment: UNP residues 22-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: btuF, yadT, b0158, JW0154 / Production host: Escherichia coli (E. coli) / References: UniProt: P37028
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 20-30% PEG400, 100 mM ADA pH6.8, 100 mM Na/K-citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2011
RadiationMonochromator: Si 111 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.466→30 Å / Num. all: 31230 / Num. obs: 30839 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.133 / Net I/σ(I): 12
Reflection shellResolution: 3.466→3.62 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 3036 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX(phenix.refine: 1.7.2_869)model building
PHENIX(phenix.refine: 1.7.2_869)refinement
SCALEPACKdata scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QI9 and 4DBL

2qi9

4dbl


Resolution: 3.466→30 Å / SU ML: 1.08 / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 2007 6.54 %RANDOM
Rwork0.2293 ---
obs0.2323 30691 96.35 %-
all-31230 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 98.539 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.069 Å2-0 Å20 Å2
2---1.8149 Å2-0 Å2
3---1.7459 Å2
Refinement stepCycle: LAST / Resolution: 3.466→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10571 0 64 0 10635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610860
X-RAY DIFFRACTIONf_angle_d1.03914803
X-RAY DIFFRACTIONf_dihedral_angle_d14.8553918
X-RAY DIFFRACTIONf_chiral_restr0.0641741
X-RAY DIFFRACTIONf_plane_restr0.0051855
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2384X-RAY DIFFRACTIONPOSITIONAL0.023
12B2384X-RAY DIFFRACTIONPOSITIONAL0.023
21C1891X-RAY DIFFRACTIONPOSITIONAL0.034
22D1891X-RAY DIFFRACTIONPOSITIONAL0.034
31C31X-RAY DIFFRACTIONPOSITIONAL0.027
32D31X-RAY DIFFRACTIONPOSITIONAL0.027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4664-3.55290.3249870.32551320X-RAY DIFFRACTION63
3.5529-3.64880.32191500.3052078X-RAY DIFFRACTION99
3.6488-3.7560.37121510.29562057X-RAY DIFFRACTION99
3.756-3.8770.32431400.27492091X-RAY DIFFRACTION99
3.877-4.01530.33551480.26622061X-RAY DIFFRACTION99
4.0153-4.17560.30721410.24942099X-RAY DIFFRACTION99
4.1756-4.36510.27151460.22262095X-RAY DIFFRACTION99
4.3651-4.59450.23961480.19282084X-RAY DIFFRACTION99
4.5945-4.88120.20841400.17812114X-RAY DIFFRACTION99
4.8812-5.25630.22571530.20912086X-RAY DIFFRACTION99
5.2563-5.78190.32741440.27882132X-RAY DIFFRACTION99
5.7819-6.61090.30431440.28142132X-RAY DIFFRACTION99
6.6109-8.30010.27431580.20852129X-RAY DIFFRACTION99
8.3001-30.14020.2531570.20152206X-RAY DIFFRACTION98
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)
10.93280.259-0.82054.08880.72072.9887-0.50040.19550.8804-0.14060.66880.0908-0.44450.0518-0.06680.8371-0.0184-0.37760.93470.29861.4806-10.359855.29438.0524
22.2005-0.5089-0.61171.28960.32713.039-0.47070.47520.4625-0.29490.3013-0.2505-0.31860.12820.24570.8662-0.4512-0.17061.40940.23881.359220.719451.616-1.452
35.1631-0.39170.13635.8709-0.61155.35470.1886-0.071-0.2947-0.1945-0.11850.24770.62830.0136-0.02910.7750.0495-0.03240.65530.03980.4699-6.150311.65417.614
44.62810.3696-0.97824.3279-0.16654.7425-0.0157-0.42550.02220.6507-0.1031-0.66680.38111.10840.05820.92060.2088-0.19681.1193-0.04710.947719.24516.891427.1666
52.2910.3305-1.4457-0.6228-0.01352.08330.61430.20291.09680.2435-0.2795-0.0326-1.0259-0.1087-0.20722.860.12860.20421.77650.73262.78483.218884.3226-13.9242
61.0509-0.0026-0.00620.76260.37690.76470.13040.69711.1926-0.97070.2401-0.3515-0.77480.3689-0.06441.2933-0.0695-0.02251.42740.33421.63076.551713.74386.9745
71.0568-0.2096-0.16040.4563-0.0561.1738-0.04040.23141.5807-0.1068-0.29830.1869-1.1146-0.5733-0.03181.21710.0808-0.58291.3990.23741.79846.37125.974532.4228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:324 )A1 - 324
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:324 )B1 - 324
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:249 )C2 - 249
4X-RAY DIFFRACTION4( CHAIN D AND RESID 2:249 )D2 - 249
5X-RAY DIFFRACTION5( CHAIN F AND RESID 22:266 )F22 - 266
6X-RAY DIFFRACTION6( CHAIN C AND RESID 301:301 )C301
7X-RAY DIFFRACTION7( CHAIN D AND RESID 301:301 )D301

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more