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- EMDB-30342: Structure of alpha6beta1 integrin in complex with laminin-511 -

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Basic information

Entry
Database: EMDB / ID: EMD-30342
TitleStructure of alpha6beta1 integrin in complex with laminin-511
Map data
Sample
  • Complex: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp
    • Protein or peptide: x 9 types
  • Ligand: x 3 types
KeywordsIntegrin / Laminin / Fv-clasp / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


laminin-5 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / ectodermal cell differentiation / integrin alpha8-beta1 complex ...laminin-5 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / ectodermal cell differentiation / integrin alpha8-beta1 complex / neuregulin binding / extracellular matrix of synaptic cleft / L1CAM interactions / Type I hemidesmosome assembly / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / trunk neural crest cell migration / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / nail development / hemidesmosome assembly / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / postsynapse organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / cell adhesion mediator activity / reactive gliosis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / glycosphingolipid binding / formation of radial glial scaffolds / Other semaphorin interactions / positive regulation of integrin-mediated signaling pathway / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / morphogenesis of embryonic epithelium / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / skin morphogenesis / CHL1 interactions / basement membrane organization / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / cardiac muscle cell differentiation / branching involved in salivary gland morphogenesis / Platelet Adhesion to exposed collagen / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / germ cell migration / leukocyte tethering or rolling / endoderm development / insulin-like growth factor I binding / cell projection organization / negative regulation of cell adhesion / myoblast fusion / regulation of epithelial cell proliferation / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / central nervous system neuron differentiation / regulation of spontaneous synaptic transmission / wound healing, spreading of epidermal cells / odontogenesis / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / heterotypic cell-cell adhesion / MET activates PTK2 signaling / Molecules associated with elastic fibres / skeletal system morphogenesis / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte migration / branching involved in ureteric bud morphogenesis
Similarity search - Function
: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV ...: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / : / Laminin/attractin EGF domain / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / TNFR/NGFR cysteine-rich region / Laminin G domain / Laminin G domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / Epidermal growth factor-like domain. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Laminin subunit alpha-5 / Integrin beta-1 / Laminin subunit beta-1 / Laminin subunit gamma-1 / Integrin alpha-6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsArimori T / Miyazaki N
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02389 Japan
Japan Agency for Medical Research and Development (AMED)19am0101075 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structural mechanism of laminin recognition by integrin.
Authors: Takao Arimori / Naoyuki Miyazaki / Emiko Mihara / Mamoru Takizawa / Yukimasa Taniguchi / Carlos Cabañas / Kiyotoshi Sekiguchi / Junichi Takagi /
Abstract: Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we ...Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we report the structures of the prototypic laminin receptor α6β1 integrin alone and in complex with three-chain laminin-511 fragment determined via crystallography and cryo-electron microscopy, respectively. The laminin-integrin interface is made up of several binding sites located on all five subunits, with the laminin γ1 chain C-terminal portion providing focal interaction using two carboxylate anchor points to bridge metal-ion dependent adhesion site of integrin β1 subunit and Asn189 of integrin α6 subunit. Laminin α5 chain also contributes to the affinity and specificity by making electrostatic interactions with large surface on the β-propeller domain of α6, part of which comprises an alternatively spliced X1 region. The propeller sheet corresponding to this region shows unusually high mobility, suggesting its unique role in ligand capture.
History
DepositionJun 22, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cec
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30342.png

Downloads & links

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Map

FileDownload / File: emd_30342.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 300 pix.
= 333.9 Å		1.11 Å/pix.
x 300 pix.
= 333.9 Å		1.11 Å/pix.
x 300 pix.
= 333.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.113 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.054479014 - 0.15038915
Average (Standard dev.)0.00052672107 (±0.0049025496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 333.90002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1131.1131.113
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z333.900333.900333.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0540.1500.001

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Supplemental data

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Sample components

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Entire : Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...

EntireName: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp
Components
  • Complex: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp
    • Protein or peptide: Integrin alpha-6
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: Laminin subunit alpha-5
    • Protein or peptide: Laminin subunit beta-1
    • Protein or peptide: Laminin subunit gamma-1
    • Protein or peptide: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH
    • Protein or peptide: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)
    • Protein or peptide: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH
    • Protein or peptide: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...

SupramoleculeName: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 286 KDa

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Macromolecule #1: Integrin alpha-6

MacromoleculeName: Integrin alpha-6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.776023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDTREDNV IRKYGDPGSL FGFSLAMHWQ LQPEDKRLLL VGAPRAEALP LQRANRTGGL YSCDITARGP CTRIEFDNDA DPTSESKED QWMGVTVQSQ GPGGKVVTCA HRYEKRQHVN TKQESRDIFG RCYVLSQNLR IEDDMDGGDW SFCDGRLRGH E KFGSCQQG ...String:
FNLDTREDNV IRKYGDPGSL FGFSLAMHWQ LQPEDKRLLL VGAPRAEALP LQRANRTGGL YSCDITARGP CTRIEFDNDA DPTSESKED QWMGVTVQSQ GPGGKVVTCA HRYEKRQHVN TKQESRDIFG RCYVLSQNLR IEDDMDGGDW SFCDGRLRGH E KFGSCQQG VAATFTKDFH YIVFGAPGTY NWKGIVRVEQ KNNTFFDMNI FEDGPYEVGG ETEHDESLVP VPANSYLGFS LD SGKGIVS KDEITFVSGA PRANHSGAVV LLKRDMKSAH LLPEHIFDGE GLASSFGYDV AVVDLNKDGW QDIVIGAPQY FDR DGEVGG AVYVYMNQQG RWNNVKPIRL NGTKDSMFGI AVKNIGDINQ DGYPDIAVGA PYDDLGKVFI YHGSANGINT KPTQ VLKGI SPYFGYSIAG NMDLDRNSYP DVAVGSLSDS VTIFRSRPVI NIQKTITVTP NRIDLRQKTA CGAPSGICLQ VKSCF EYTA NPAGYNPSIS IVGTLEAEKE RRKSGLSSRV QFRNQGSEPK YTQELTLKRQ KQKVCMEETL WLQDNIRDKL RPIPIT ASV EIQEPSSRRR VNSLPEVLPI LNSDEPKTAH IDVHFLKEGC GDDNVCNSNL KLEYKGSLEN LYFQ

UniProtKB: Integrin alpha-6

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.51093 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV ...String:
QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTSPFS YKNVLSLTNK GEVFNELVGK QRISGNLDSP EGGFDAIMQV AV CGSLIGW RNVTRLLVFS TDAGFHFAGD GKLGGIVLPN DGQCHLENNM YTMSHYYDYP SIAHLVQKLS ENNIQTIFAV TEE FQPVYK ELKNLIPKSA VGTLSANSSN VIQLIIDAYN SLSSEVILEN GKLSEGVTIS YKSYCKNGVN GTGENGRKCS NISI GDEVQ FEISITSNKC PKKDSDSFKI RPLGFTEEVE VILQYICECE GGLENLYFQ

UniProtKB: Integrin beta-1

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Macromolecule #3: Laminin subunit alpha-5

MacromoleculeName: Laminin subunit alpha-5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.414203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GENVERWQGQ YEGLRGQDLG QAVLDAGHSV STLEKTLPQL LAKLSILENR GVHNASLALS ASIGRVRELC AQARGAASKV KVPMKFNGR SGVQLRTPRD LADLAAYTAL KFYLQGPEPE PGQGTEDRFV MYMGSRQATG DYMGVSLRDK KVHWVYQLGE A GPAVLSID ...String:
GENVERWQGQ YEGLRGQDLG QAVLDAGHSV STLEKTLPQL LAKLSILENR GVHNASLALS ASIGRVRELC AQARGAASKV KVPMKFNGR SGVQLRTPRD LADLAAYTAL KFYLQGPEPE PGQGTEDRFV MYMGSRQATG DYMGVSLRDK KVHWVYQLGE A GPAVLSID EDIGEQFAAV SLDRTLQFGH MSVTVERQMI QETKGDTVAP GAEGLLNLRP DDFVFYVGGY PSTFTPPPLL RF PGYRGCI EMDTLNEEVV SLYNFERTFQ LDTAVDRPCA RSKSTGDPWL TDGSYLDGTG FARISFDSQI STTKRFEQEL RLV SYSGVL FFLKQQSQFL CLAVQEGSLV LLYDFGAGLK KAVPLQPPPP LTSASKAIQV FLLGGSRKRV LVRVERATVY SVEQ DNDLE LADAYYLGGV PPDQLPPSLR RLFPTGGSVR GCVKGIKALG KYVDLKRLNT TGVSAGCTAD LLVGRAMTFH GHGFL RLAL SNVAPLTGNV YSGFGFHSAQ DSALLYYRAS PDGLCQVSLQ QGRVSLQLLR TEVKTQAGFA DGAPHYVAFY SNATGV WLY VDDQLQQMKP HRGPPPELQP QPEGPPRLLL GGLPESGTIY NFSGCISNVF VQRLLGPQRV FDLQQNLGSV NVSTGCA PA LQAQTPGLGP RGLQATARKA SRRSRQPARH PA

UniProtKB: Laminin subunit alpha-5

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Macromolecule #4: Laminin subunit beta-1

MacromoleculeName: Laminin subunit beta-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.552753 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GDARRKAEML QNEAKTLLAQ ANSKLQLLKD LERKYEDNQR YLEDKAQELA RLEGEVRSLL KDISQKVAVY STCL

UniProtKB: Laminin subunit beta-1

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Macromolecule #5: Laminin subunit gamma-1

MacromoleculeName: Laminin subunit gamma-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.483724 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GDTVDLNKLN EIEGTLNKAK DEMKVSDLDR KVSDLENEAK KQEAAIMDYN RDIEEIMKCI RNLEDIRKTL PSGCFNTPSI EKP

UniProtKB: Laminin subunit gamma-1

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Macromolecule #6: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH

MacromoleculeName: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH / type: protein_or_peptide / ID: 6 / Details: chimera of TS2/16 VH(S112C)-SARAH / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.463992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVKLVESGG GLVKPGGSLK LSCAASGFTF SSYTMSWVRQ TPEKRLEWVA TISSGGSYTY YPDSVKGRFT ISRDKAKNTL YLQMGSLKS EDTAMYYCTR IGYDEDYAMD HWGQGTSVTV CSGSDYEFLK SWTVEDLQKR LLALDPMMEQ EIEEIRQKYQ S KRQPILDA IEAK

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Macromolecule #7: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)

MacromoleculeName: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C) / type: protein_or_peptide / ID: 7 / Details: chimera of TS2/16 VL-SARAH(S37C) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.270742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMQIVVTQ RPTTMAASPG DKIIITCSVS SIISSNYLHW YSQKPGFSPK LLIYRTSNLA SGVPPRFSGS GSGTSYSLTI GTMEAEDVA TYYCQQGSDI PLTFGDGTKL DLKRGSDYEF LKSWTVEDLQ KRLLALDPMM EQEIEEIRQK YQCKRQPILD A IEAK

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Macromolecule #8: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH

MacromoleculeName: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH / type: protein_or_peptide / ID: 8 / Details: chimera of HUTS-4 VH(S112C)-SARAH / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.760207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQVTLKESGP GILQPSQTLS LTCSFSGFSL STSGMGVSWI RQPSGKGLEW LAHIYWDDDK RYHPSLKSRL TISKDTSSNQ VFLKITSVD TADTATYYCA RSIYDGYYDY FDVWGAGTTV TVCSGSDYEF LKSWTVEDLQ KRLLALDPMM EQEIEEIRQK Y QSKRQPIL DAIEAK

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Macromolecule #9: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)

MacromoleculeName: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
type: protein_or_peptide / ID: 9 / Details: chimera of HUTS-4 VL(C87Y)-SARAH(S37C) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.701023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIVLSQSPA ILSASPGEKV TMTCRATSSV TYMHWYQQKP GSSPKPWIYA TSNLASGVPA RFSGSGSGTS YSLTISRVEA ADAATYYCQ QWTSNPPTFG GGTKLEIKRG SDYEFLKSWT VEDLQKRLLA LDPMMEQEIE EIRQKYQCKR QPILDAIEAK

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #13: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 13 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

Concentration0.07 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
1.0 mMMnCl2manganese chloride
0.1 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: MOLYBDENUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 7768 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2660283
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 429521
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 130000 / Software - Name: RELION (ver. 3.0)

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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

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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

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