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- PDB-7cea: Crystal structure of HUTS-4 Fv-clasp fragment -

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Basic information

Entry
Database: PDB / ID: 7cea
TitleCrystal structure of HUTS-4 Fv-clasp fragment
Components
  • HUTS-4 VH(S112C)-SARAH
  • HUTS-4 VL(C87Y)-SARAH(S37C)
KeywordsIMMUNE SYSTEM / Antibody fragment / Fv-clasp / Integrin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsArimori, T. / Takagi, J.
Funding support Japan, 2items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUTS-4 VH(S112C)-SARAH
B: HUTS-4 VL(C87Y)-SARAH(S37C)


Theoretical massNumber of molelcules
Total (without water)37,4612
Polymers37,4612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-38 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.367, 88.367, 78.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Antibody HUTS-4 VH(S112C)-SARAH


Mass: 19760.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of HUTS-4 VH(S112C)-SARAH
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
#2: Antibody HUTS-4 VL(C87Y)-SARAH(S37C)


Mass: 17701.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of HUTS-4 VL(C87Y)-SARAH(S37C)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli)
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.26 M ammonium sulfate, 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→44.183 Å / Num. obs: 11865 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 69.53 Å2 / CC1/2: 0.999 / Rsym value: 0.104 / Net I/σ(I): 17.77
Reflection shellResolution: 2.55→2.7 Å / Num. unique obs: 1860 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qq9, 4kaq, 5xct

3qq9

4kaq

5xct


Resolution: 2.55→34.79 Å / SU ML: 0.3834 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.7576 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 589 5.01 %
Rwork0.2519 11166 -
obs0.2527 11755 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.34 Å2
Refinement stepCycle: LAST / Resolution: 2.55→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 0 0 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512626
X-RAY DIFFRACTIONf_angle_d0.86723562
X-RAY DIFFRACTIONf_chiral_restr0.0467390
X-RAY DIFFRACTIONf_plane_restr0.0057450
X-RAY DIFFRACTIONf_dihedral_angle_d15.89481588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.80.43241430.42532722X-RAY DIFFRACTION97.88
2.8-3.210.42511460.35022747X-RAY DIFFRACTION99.08
3.21-4.040.32521470.27422787X-RAY DIFFRACTION99.05
4.04-34.790.19681530.20292910X-RAY DIFFRACTION99.71
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)
13.02369654772-0.316914459742-1.461700400872.677417586551.045727897612.02308692788-0.049158708010.5573097473310.285017660565-0.08550105048990.215711546122-0.011161726129-0.323769386132-0.115269397873-0.1160909027320.944125671707-0.137942701372-0.05477719572640.7931470515650.08342387104090.63998912664836.2537315405-26.98288570030.616860006236
21.888854081720.517720282454-0.2524012783013.150002085780.8249181232991.968893380220.1054168727560.07152718954190.1860746175590.08276697828480.1287521403790.477586861232-0.202312442864-0.567769350396-0.1234806483590.9564870062940.07516381905920.04109605308951.053299334750.08113797326810.97275384849212.0867625295-31.605992268319.791201679
32.226260131241.40991504441-0.626518192862.5651812690.5631495326241.38344410757-0.4749034776850.980759565242-0.650417909691-0.5591938707780.499018512654-0.3157453226470.61225993624-0.6398636938250.0281461178170.931385539394-0.269823324635-0.006744858151821.05493469443-0.1436919463530.74990674123335.5357887185-48.7612081025-2.03599990432
41.471363443040.355517291883-0.2680767364642.21446094888-0.323625132071.4950916365-0.2118761080930.347574429672-0.004492761725330.157025090550.425551409088-0.1416915653050.0165926923574-0.0149158046862-0.1063476550230.9194830937522.96084305438E-5-0.06149966708590.932949552597-0.01069241368130.84280653320321.2967381794-34.623195683716.7316441814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 164 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )
4X-RAY DIFFRACTION4chain 'B' and (resid 117 through 159 )

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