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- PDB-7bzz: Crystal structure of the SRCR domain of mouse SCARA5 -

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Basic information

Entry
Database: PDB / ID: 7bzz
TitleCrystal structure of the SRCR domain of mouse SCARA5
ComponentsScavenger receptor class A member 5
KeywordsMETAL BINDING PROTEIN / SCARA5 / SRCR / SR class A / scavenger receptor / ferritin
Function / homology
Function and homology information


ferritin receptor activity / iron ion transmembrane transport / scavenger receptor activity / plasma membrane => GO:0005886 / protein homotrimerization / endocytosis / endocytic vesicle membrane / cellular response to heat / intracellular iron ion homeostasis / external side of plasma membrane ...ferritin receptor activity / iron ion transmembrane transport / scavenger receptor activity / plasma membrane => GO:0005886 / protein homotrimerization / endocytosis / endocytic vesicle membrane / cellular response to heat / intracellular iron ion homeostasis / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
Scavenger receptor class A member 5 / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Scavenger receptor class A member 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsYu, B. / He, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 91957102 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Interactions of ferritin with scavenger receptor class A members.
Authors: Yu, B. / Cheng, C. / Wu, Y. / Guo, L. / Kong, D. / Zhang, Z. / Wang, Y. / Zheng, E. / Liu, Y. / He, Y.
History
DepositionApr 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scavenger receptor class A member 5
D: Scavenger receptor class A member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,35610
Polymers25,6732
Non-polymers6838
Water68538
1
A: Scavenger receptor class A member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1785
Polymers12,8361
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-8 kcal/mol
Surface area5850 Å2
MethodPISA
2
D: Scavenger receptor class A member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1785
Polymers12,8361
Non-polymers3414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-8 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.795, 39.795, 132.173
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 11 or (resid 12...
21(chain D and (resid 1 through 108 or (resid 109...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 11 or (resid 12...A1 - 11
121(chain A and (resid 1 through 11 or (resid 12...A12
131(chain A and (resid 1 through 11 or (resid 12...A384 - 492
141(chain A and (resid 1 through 11 or (resid 12...A384 - 492
151(chain A and (resid 1 through 11 or (resid 12...A384 - 492
161(chain A and (resid 1 through 11 or (resid 12...A384 - 492
211(chain D and (resid 1 through 108 or (resid 109...D1 - 108
221(chain D and (resid 1 through 108 or (resid 109...D109
231(chain D and (resid 1 through 108 or (resid 109...D384 - 492
241(chain D and (resid 1 through 108 or (resid 109...D384 - 492
251(chain D and (resid 1 through 108 or (resid 109...D384 - 492
261(chain D and (resid 1 through 108 or (resid 109...D384 - 492

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Components

#1: Protein Scavenger receptor class A member 5


Mass: 12836.312 Da / Num. of mol.: 2 / Fragment: SRCR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scara5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8K299
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) polyethylene glycol 3350, 0.2M ammonium sulfate (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 8067 / % possible obs: 99.91 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 26.22
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.326 / Num. unique obs: 1040

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J02

6j02


Resolution: 2.501→27.145 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2.07 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2431 803 9.99 %
Rwork0.1977 --
obs0.2024 8038 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.89 Å2 / Biso mean: 52.1607 Å2 / Biso min: 27.34 Å2
Refinement stepCycle: final / Resolution: 2.501→27.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 37 38 1777
Biso mean--70.04 50.83 -
Num. residues----218
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A862X-RAY DIFFRACTIONPOSITIONAL0.166
12D862X-RAY DIFFRACTIONPOSITIONAL0.166
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.501-2.6570.27931330.2301122799
2.657-2.8620.28151290.20411186100
2.862-3.14960.28491380.21811191100
3.1496-3.60450.23231320.19631232100
3.6045-4.53780.22011300.17481203100
4.5378-27.1450.2341410.2021119699
Refinement TLS params.Method: refined / Origin x: 9.1253 Å / Origin y: 7.0865 Å / Origin z: -17.8753 Å
111213212223313233
T0.2637 Å2-0.0911 Å2-0.0188 Å2-0.3786 Å2-0.0112 Å2--0.2657 Å2
L1.0511 °20.0912 °2-1.2195 °2-0.8545 °2-0.7179 °2--3.8641 °2
S-0.1369 Å °-0.2401 Å °-0.0961 Å °-0.191 Å °0.1223 Å °-0.0417 Å °0.0791 Å °0.0472 Å °0.032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA384 - 492
2X-RAY DIFFRACTION1allA584
3X-RAY DIFFRACTION1allB4 - 12
4X-RAY DIFFRACTION1allD384 - 492
5X-RAY DIFFRACTION1allD584
6X-RAY DIFFRACTION1allS1 - 44

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