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- PDB-4r9u: Structure of vitamin B12 transporter BtuCD in a nucleotide-bound ... -

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Basic information

Entry
Database: PDB / ID: 4r9u
TitleStructure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state
Components
  • Vitamin B12 import ATP-binding protein BtuD
  • Vitamin B12 import system permease protein BtuC
KeywordsHYDROLASE / nucleotide / AMPPNP / ATP binding cassette / membrane protein / ABC transporter / BtuF / inner 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 / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity ...ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...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, BtuC-like / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.785 Å
AuthorsKorkhov, V.M. / Mireku, S.A. / Veprintsev, D.B. / Locher, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F.
Authors: Korkhov, V.M. / Mireku, S.A. / Veprintsev, D.B. / Locher, K.P.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,12012
Polymers125,1414
Non-polymers1,9798
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-90 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)372.850, 113.210, 69.430
Angle α, β, γ (deg.)90.00, 94.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Vitamin B12 import system permease protein BtuC


Mass: 35484.273 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, EC: 3.6.3.33
#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: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 5.83 Å3/Da / Density % sol: 78.91 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG2000MME (14-18%), NaCl (1.2 M), ADA (100 mM, pH 6.9), VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationMonochromator: double crystal fixed-exit, Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.785→30 Å / Num. all: 64150 / Num. obs: 49823 / % possible obs: 88.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.4 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.85141.5
2.85-2.91153.5
2.91-2.98161.9
2.98-3.04170.8
3.04-3.12179.9
3.12-3.2190.2
3.2-3.3196.3
3.3-3.41199.4
3.41-3.53199.9
3.53-3.671100
3.67-3.831100
3.83-4.041100
4.04-4.291100
4.29-4.621100
4.62-5.081100
5.08-5.811100
5.81-7.31100
7.3-301100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FI3

4fi3


Resolution: 2.785→29.514 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1972 3.96 %random
Rwork0.2169 ---
obs0.2181 49823 69.22 %-
all-64150 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.785→29.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8664 0 128 0 8792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118967
X-RAY DIFFRACTIONf_angle_d1.5112208
X-RAY DIFFRACTIONf_dihedral_angle_d18.833222
X-RAY DIFFRACTIONf_chiral_restr0.0631448
X-RAY DIFFRACTIONf_plane_restr0.0091504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7854-2.8550.591990.5579220X-RAY DIFFRACTION5
2.855-2.93220.5414210.4516610X-RAY DIFFRACTION12
2.9322-3.01840.4109510.3551177X-RAY DIFFRACTION24
3.0184-3.11570.4045720.36171995X-RAY DIFFRACTION41
3.1157-3.22690.38711240.35152621X-RAY DIFFRACTION54
3.2269-3.35590.39651140.32173255X-RAY DIFFRACTION66
3.3559-3.50840.28581700.29053763X-RAY DIFFRACTION77
3.5084-3.69310.29611730.25984451X-RAY DIFFRACTION90
3.6931-3.9240.26332040.23884885X-RAY DIFFRACTION99
3.924-4.22620.2412130.20454938X-RAY DIFFRACTION100
4.2262-4.650.19431990.17554964X-RAY DIFFRACTION100
4.65-5.31940.21442110.18184949X-RAY DIFFRACTION100
5.3194-6.6890.252030.22894968X-RAY DIFFRACTION100
6.689-29.51530.19342080.16235055X-RAY DIFFRACTION100
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)
10.71360.0841-0.23620.3740.48730.8033-0.0445-0.21350.22920.02260.11390.01190.06020.00340.13950.44060.12210.03950.2388-0.03370.5483-69.324750.640815.0983
20.62160.0242-0.15560.56450.13380.8291-0.03820.3266-0.3294-0.04870.16050.05340.08940.19830.28360.3387-0.3388-0.1258-0.482-0.05040.4769-67.796728.4525-9.1524
30.92740.4451-0.05950.28390.0060.51390.0099-1.10890.05790.2856-0.0764-0.1290.02910.373-0.01790.46220.1377-0.03051.1282-0.05980.3068-26.400638.027921.6596
40.8783-0.28140.03070.2132-0.00890.3879-0.07380.5315-0.2133-0.0755-0.0446-0.01560.13730.2271-0.03590.38180.0321-0.00240.8124-0.13990.3047-23.260635.7189-4.9742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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