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- PDB-6ort: Crystal Structure of Bos taurus Mxra8 Ectodomain -

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Basic information

Entry
Database: PDB / ID: 6ort
TitleCrystal Structure of Bos taurus Mxra8 Ectodomain
ComponentsMatrix remodeling-associated protein 8
KeywordsMEMBRANE PROTEIN / Receptor / Chikungunya virus / Cow / Bovine / Alphavirus / Moo insertion / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / ciliary membrane / bicellular tight junction / membrane => GO:0016020 / cell adhesion / nucleus / cytoplasm
Similarity search - Function
Matrix remodeling-associated protein 8 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Matrix remodeling-associated protein 8
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFremont, D.H. / Kim, A.S. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis.
Authors: Kim, A.S. / Zimmerman, O. / Fox, J.M. / Nelson, C.A. / Basore, K. / Zhang, R. / Durnell, L. / Desai, C. / Bullock, C. / Deem, S.L. / Oppenheimer, J. / Shapiro, B. / Wang, T. / Cherry, S. / ...Authors: Kim, A.S. / Zimmerman, O. / Fox, J.M. / Nelson, C.A. / Basore, K. / Zhang, R. / Durnell, L. / Desai, C. / Bullock, C. / Deem, S.L. / Oppenheimer, J. / Shapiro, B. / Wang, T. / Cherry, S. / Coyne, C.B. / Handley, S.A. / Landis, M.J. / Fremont, D.H. / Diamond, M.S.
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix remodeling-associated protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7125
Polymers32,3671
Non-polymers3454
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-22 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.530, 77.530, 242.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

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Components

#1: Protein Matrix remodeling-associated protein 8 / Limitrin


Mass: 32366.984 Da / Num. of mol.: 1 / Fragment: UNP residues 24-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: MXRA8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q148M6
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES, pH 8.0, 6% w/v PEG6000, 1.0 M lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Apr 16, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.47 Å / Num. obs: 20081 / % possible obs: 99.91 % / Redundancy: 71.1 % / CC1/2: 1 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.146 / Χ2: 0.99 / Net I/σ(I): 49.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 76.6 % / Rmerge(I) obs: 2.234 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1939 / CC1/2: 0.93 / Rrim(I) all: 2.248 / Χ2: 0.94 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDS20180126data reduction
Aimless0.5.26data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NK3

6nk3


Resolution: 2.3→44.981 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1004 5 %
Rwork0.218 19075 -
obs0.2193 20079 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.82 Å2 / Biso mean: 50.9892 Å2 / Biso min: 21.07 Å2
Refinement stepCycle: final / Resolution: 2.3→44.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 18 117 2364
Biso mean--61.11 49.77 -
Num. residues----277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.42140.30681420.26492650100
2.4214-2.57310.35381360.27272648100
2.5731-2.77170.33561440.26382677100
2.7717-3.05060.26191380.24912666100
3.0506-3.49190.24471450.20882719100
3.4919-4.39880.191440.18732753100
4.3988-44.9810.22431550.20922962100
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)
12.43311.1606-2.72334.6977-0.10116.79410.2427-0.02880.35220.0970.1320.5542-1.4663-0.2147-0.37550.7087-0.26070.04690.3069-0.0310.440413.129734.427144.7153
2-0.02881.12451.6919-0.28562.6496.0880.2966-0.29640.15330.3196-0.3016-0.047-0.3711-0.6933-0.06590.71930.046-0.04910.3266-0.01260.41310.833521.6962126.5351
30.32510.4961-0.12260.8708-0.43420.66570.57530.37150.7721-0.4774-0.0270.2275-1.24570.0018-0.23940.9034-0.0865-0.03290.19110.50591.334810.502732.690397.5709
44.59741.6866-2.75373.4543-1.79727.04290.00170.12750.3990.0099-0.1935-0.4426-0.7621-0.34690.09510.53760.1917-0.13680.4189-0.02930.35422.288919.1191106.5448
52.5841-0.57360.13352.3970.65854.51470.099-1.08010.12780.208-0.3567-0.295-0.0643-0.18370.3310.50880.04780.06450.40330.16590.434-11.30236.7345114.6523
62.0155-0.8381-0.49111.63141.21445.44660.11660.00150.26260.0627-0.0387-0.2946-0.53140.3404-0.08860.3729-0.0057-0.0850.1652-0.0030.411311.605316.3986107.2543
73.9660.07820.69486.44560.40644.76670.1674-0.48030.11840.4984-0.0081-0.2126-0.3691-0.0082-0.16280.447-0.1372-0.00750.26720.04830.24628.601321.7862150.8139
86.4755.24775.51758.0635.79178.5759-0.01110.186-0.0378-0.26580.0894-0.1921-0.48150.41030.02450.4582-0.155-0.02080.2040.04950.27813.342423.4858142.2922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 49 )A33 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 78 )A50 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 85 )A79 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 94 )A86 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 112 )A95 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 219 )A113 - 219
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 283 )A220 - 283
8X-RAY DIFFRACTION8chain 'A' and (resid 284 through 309 )A284 - 309

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