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- EMDB-41845: Gaussian mixture model based single particle refinement - ABC tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-41845
TitleGaussian mixture model based single particle refinement - ABC transporter (inhibitor-bound ABCG2 from EMPIAR-10374)
Map data
Sample
  • Complex: inhibitor-bound ABCG2
    • Protein or peptide: Broad substrate specificity ATP-binding cassette transporter ABCG2
    • Protein or peptide: 5D3 Fab light chain variable domain
    • Protein or peptide: 5D3 Fab heavy chain variable domain
    • Protein or peptide: FAB heavy chain constant domain
    • Protein or peptide: Fab light chain constant domain
KeywordsABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


biotin transmembrane transporter activity / biotin transport / riboflavin transport / riboflavin transmembrane transporter activity / renal urate salt excretion / urate metabolic process / urate transmembrane transporter activity / Abacavir transmembrane transport / organic anion transport / external side of apical plasma membrane ...biotin transmembrane transporter activity / biotin transport / riboflavin transport / riboflavin transmembrane transporter activity / renal urate salt excretion / urate metabolic process / urate transmembrane transporter activity / Abacavir transmembrane transport / organic anion transport / external side of apical plasma membrane / organic anion transmembrane transporter activity / xenobiotic transport across blood-brain barrier / export across plasma membrane / ABC-type xenobiotic transporter / Paracetamol ADME / Ciprofloxacin ADME / transepithelial transport / cellular detoxification / ABC-type xenobiotic transporter activity / NFE2L2 regulating MDR associated enzymes / Heme biosynthesis / Heme degradation / lipid transport / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transport across blood-brain barrier / ATPase-coupled transmembrane transporter activity / mitochondrial membrane / brush border membrane / Iron uptake and transport / transmembrane transport / membrane raft / apical plasma membrane / ATP hydrolysis activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Broad substrate specificity ATP-binding cassette transporter ABCG2
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsChen M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH125285 United States
CitationJournal: Nat Methods / Year: 2024
Title: Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models.
Authors: Muyuan Chen / Michael F Schmid / Wah Chiu /
Abstract: Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian ...Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.
History
DepositionSep 5, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41845.png

Downloads & links

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Map

FileDownload / File: emd_41845.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-9.731674 - 26.853702999999999
Average (Standard dev.)0.074904196 (±1.0001292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41845_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41845_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : inhibitor-bound ABCG2

EntireName: inhibitor-bound ABCG2
Components
  • Complex: inhibitor-bound ABCG2
    • Protein or peptide: Broad substrate specificity ATP-binding cassette transporter ABCG2
    • Protein or peptide: 5D3 Fab light chain variable domain
    • Protein or peptide: 5D3 Fab heavy chain variable domain
    • Protein or peptide: FAB heavy chain constant domain
    • Protein or peptide: Fab light chain constant domain

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Supramolecule #1: inhibitor-bound ABCG2

SupramoleculeName: inhibitor-bound ABCG2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Re-refinement from EMPIAR-10374
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Broad substrate specificity ATP-binding cassette transporter ABCG2

MacromoleculeName: Broad substrate specificity ATP-binding cassette transporter ABCG2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.385852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSNVEVFI PVSQGNTNGF PATASNDLKA FTEGAVLSFH NICYRVKLKS GFLPCRKPVE KEILSNINGI MKPGLNAILG PTGGGKSSL LDVLAARKDP SGLSGDVLIN GAPRPANFKC NSGYVVQDDV VMGTLTVREN LQFSAALRLA TTMTNHEKNE R INRVIQEL ...String:
MSSSNVEVFI PVSQGNTNGF PATASNDLKA FTEGAVLSFH NICYRVKLKS GFLPCRKPVE KEILSNINGI MKPGLNAILG PTGGGKSSL LDVLAARKDP SGLSGDVLIN GAPRPANFKC NSGYVVQDDV VMGTLTVREN LQFSAALRLA TTMTNHEKNE R INRVIQEL GLDKVADSKV GTQFIRGVSG GERKRTSIGM ELITDPSILF LDEPTTGLDS STANAVLLLL KRMSKQGRTI IF SIHQPRY SIFKLFDSLT LLASGRLMFH GPAQEALGYF ESAGYHCEAY NNPADFFLDI INGDSTAVAL NREEDFKATE IIE PSKQDK PLIEKLAEIY VNSSFYKETK AELHQLSGGE KKKKITVFKE ISYTTSFCHQ LRWVSKRSFK NLLGNPQASI AQII VTVVL GLVIGAIYFG LKNDSTGIQN RAGVLFFLTT NQCFSSVSAV ELFVVEKKLF IHEYISGYYR VSSYFLGKLL SDLLP MRML PSIIFTCIVY FMLGLKPKAD AFFVMMFTLM MVAYSASSMA LAIAAGQSVV SVATLLMTIC FVFMMIFSGL LVNLTT IAS WLSWLQYFSI PRYGFTALQH NEFLGQNFCP GLNATGNNPC NYATCTGEEY LVKQGIDLSP WGLWKNHVAL ACMIVIF LT IAYLKLLFLK KYS

UniProtKB: Broad substrate specificity ATP-binding cassette transporter ABCG2

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Macromolecule #2: 5D3 Fab light chain variable domain

MacromoleculeName: 5D3 Fab light chain variable domain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.594016 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVLTQSPSS FSVSLGDRVT ISCKASGYIL NRLAWYQQKP GNAPRLLISG ATSLETGFPS RFSGTGSGKD YTLSISSLQT EDVGTYYCQ QYWSTPWTFG GGTKLEIRRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVLTQSPSS FSVSLGDRVT ISCKASGYIL NRLAWYQQKP GNAPRLLISG ATSLETGFPS RFSGTGSGKD YTLSISSLQT EDVGTYYCQ QYWSTPWTFG GGTKLEIRRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #3: 5D3 Fab heavy chain variable domain

MacromoleculeName: 5D3 Fab heavy chain variable domain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.843633 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QVQLQESGPG LVKPSQSLSL TCTVTGFSIT SDYAWNWIRQ FPGKKLEWMG YINFDGGTTY NPSLRGRISI TRDTSKNQFF LQLRSVTPE DTATYYCATF YGAKGTLDYW GQGTSVTVSS AKTTPPSVYP LAPVCGDTSG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG ...String:
QVQLQESGPG LVKPSQSLSL TCTVTGFSIT SDYAWNWIRQ FPGKKLEWMG YINFDGGTTY NPSLRGRISI TRDTSKNQFF LQLRSVTPE DTATYYCATF YGAKGTLDYW GQGTSVTVSS AKTTPPSVYP LAPVCGDTSG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VTSSTWPSQS ITCNVAHPAS STKVDKKIEP RGP

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Macromolecule #4: FAB heavy chain constant domain

MacromoleculeName: FAB heavy chain constant domain / type: protein_or_peptide / ID: 4
Details: The Fab domains were not resolved in the original structure and, therefore, were not modeled. With the implementation of an improved method, we can now resolve the domains within the CryoEM ...Details: The Fab domains were not resolved in the original structure and, therefore, were not modeled. With the implementation of an improved method, we can now resolve the domains within the CryoEM density map. However, given the absence of FAB information in the original structure, we opted to fit a representative FAB structure, utilizing PDB ID 7FAB as a reference.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.98684 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVQLEQSGPG LVRPSQTLSL TCTVSGTSFD DYYWTWVRQP PGRGLEWIGY VFYTGTTLLD PSLRGRVTML VNTSKNQFSL RLSSVTAAD TAVYYCARNL IAGGIDVWGQ GSLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
AVQLEQSGPG LVRPSQTLSL TCTVSGTSFD DYYWTWVRQP PGRGLEWIGY VFYTGTTLLD PSLRGRVTML VNTSKNQFSL RLSSVTAAD TAVYYCARNL IAGGIDVWGQ GSLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEP

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Macromolecule #5: Fab light chain constant domain

MacromoleculeName: Fab light chain constant domain / type: protein_or_peptide / ID: 5
Details: The Fab domains were not resolved in the original structure and, therefore, were not modeled. With the implementation of an improved method, we can now resolve the domains within the CryoEM ...Details: The Fab domains were not resolved in the original structure and, therefore, were not modeled. With the implementation of an improved method, we can now resolve the domains within the CryoEM density map. However, given the absence of FAB information in the original structure, we opted to fit a representative FAB structure, utilizing PDB ID 7FAB as a reference.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.866355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDYT LTISSLQPED FATYYCQQD GWSLITFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD ...String:
QMTQSPSSLS ASVGDRVTIT CRASQSVSSA VAWYQQKPGK APKLLIYSAS SLYSGVPSRF SGSRSGTDYT LTISSLQPED FATYYCQQD GWSLITFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3953

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.99) / Number images used: 284831
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6eti

source_name: PDB, initial_model_type: experimental model

7fab

source_name: PDB, initial_model_type: experimental model
Output model

PDB-8u2c:
Gaussian mixture model based single particle refinement - ABC transporter (inhibitor-bound ABCG2 from EMPIAR-10374)

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