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- PDB-6iom: Crystal structure of human C4.4A -

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Basic information

Entry
Database: PDB / ID: 6iom
TitleCrystal structure of human C4.4A
ComponentsLy6/PLAUR domain-containing protein 3
KeywordsCELL ADHESION / uPAR / three-fingered fold / LU domain
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of smooth muscle cell apoptotic process / side of membrane / laminin binding / cell-matrix adhesion / extracellular space / extracellular region / plasma membrane
Similarity search - Function
u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Ly6/PLAUR domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsHuang, M.D. / Jiang, Y.B. / Yuan, C. / Lin, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670739 China
National Natural Science Foundation of China31570745 China
National Natural Science Foundation of China31370737 China
CitationJournal: Int J Biol Sci / Year: 2020
Title: Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain
Authors: Jiang, Y.B. / Lin, L. / Chen, S. / Jiang, L.G. / Kriegbaum, M.C. / Gardsvoll, H. / Hansen, L.V. / Li, J. / Ploug, M. / Yuan, C. / Huang, M.D.
History
DepositionOct 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 4, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_abbrev ..._chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _citation.country / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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: Ly6/PLAUR domain-containing protein 3
B: Ly6/PLAUR domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2429
Polymers42,2882
Non-polymers1,9557
Water00
1
A: Ly6/PLAUR domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2325
Polymers21,1441
Non-polymers1,0884
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ly6/PLAUR domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0114
Polymers21,1441
Non-polymers8673
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.055, 120.156, 169.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Ly6/PLAUR domain-containing protein 3 / GPI-anchored metastasis-associated protein C4.4A homolog / Matrigel-induced gene C4 protein / MIG-C4


Mass: 21143.783 Da / Num. of mol.: 2 / Fragment: UNP residues 31-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C4.4A / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O95274
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 5
Source method: isolated from a genetically manipulated source
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
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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.6
Details: 22.5%(w/v) polyethylene glycol 4000, 0.1M citric acid in pH 3.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9196 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.59→49.309 Å / Num. obs: 18403 / % possible obs: 99.49 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 37.58
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.69 / Num. unique obs: 1763

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ION

6ion


Resolution: 2.594→49.309 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.2562 922 5.01 %
Rwork0.1976 --
obs0.2007 18391 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.594→49.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 98 0 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013004
X-RAY DIFFRACTIONf_angle_d1.4134097
X-RAY DIFFRACTIONf_dihedral_angle_d4.461768
X-RAY DIFFRACTIONf_chiral_restr0.073484
X-RAY DIFFRACTIONf_plane_restr0.008534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5936-2.73030.36671140.29032420X-RAY DIFFRACTION98
2.7303-2.90130.3091280.252472X-RAY DIFFRACTION100
2.9013-3.12520.29851350.23542459X-RAY DIFFRACTION100
3.1252-3.43960.28811310.22692500X-RAY DIFFRACTION100
3.4396-3.9370.26411390.19462481X-RAY DIFFRACTION100
3.937-4.95880.21851320.15622529X-RAY DIFFRACTION100
4.9588-41.15460.23481430.18642608X-RAY DIFFRACTION99
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)
16.32772.25012.31297.66872.19534.7865-0.53620.1608-0.42420.3355-0.1111-0.110.266-1.2280.20630.7094-0.07-0.12460.445-0.05960.574631.149240.665377.5022
23.66624.1943-2.60068.4431-1.13232.7546-0.58180.9447-0.2726-0.00670.23520.1846-0.94780.13750.54431.0703-0.1235-0.13960.6326-0.09540.800226.538544.043169.1774
38.9340.74463.00624.56662.66556.2202-0.1455-1.0718-0.84940.9467-0.20960.51560.49890.0469-0.38520.614-0.1387-0.01340.0429-0.09320.661832.201535.758280.6959
44.45971.9324-1.68095.3907-4.98234.9448-0.34740.02270.18370.88320.43790.2904-0.4851-0.4662-0.34290.6052-0.0954-0.05490.3083-0.05340.391232.903552.81576.5684
53.05460.0762-0.34213.1315-4.85288.507-0.46540.36210.9584-0.08130.25990.1016-0.4629-0.6737-0.22090.617-0.2191-0.19090.43120.08140.478731.752851.962570.9757
61.1808-1.70012.24424.598-6.59029.51540.0681-0.05960.52780.91260.1059-0.3316-1.3773-0.13620.02530.9807-0.0343-0.09610.426-0.07390.467236.724653.290786.2806
72.56570.9732-1.85237.2859-7.28617.8073-0.82680.45270.2039-0.10740.37090.0365-1.25840.7310.03920.708-0.1495-0.14610.46150.10290.639238.063866.304970.1065
87.33091.4109-1.70962.26421.24431.6509-0.0008-0.03770.1371.0055-0.00890.58440.3717-0.1102-0.48880.9834-0.0615-0.06910.23190.07960.430332.832555.007480.4127
97.09852.6345-0.03128.8238-3.05517.00490.0442-0.37190.23841.1925-0.10421.1195-0.1985-0.64820.13450.8507-0.04970.10120.3608-0.06260.542228.439443.266986.7504
107.1703-0.86346.30062.9296-0.69536.03520.6841-0.1868-0.50670.62191.44381.29410.6665-1.0969-1.15510.37490.17370.11390.6487-0.03270.735824.45955.646173.234
110.7576-0.77660.77480.9212-1.04481.2505-0.13710.45450.43220.22460.45950.28730.0198-0.70060.60850.56290.3871-0.41951.02081.08710.626230.200874.91855.5231
127.09135.1525-7.30377.6269-5.97647.6445-0.24791.22980.361-1.26310.95110.2074-0.3765-0.64040.0511.2188-0.5263-0.36970.96370.1880.555535.502961.574355.3699
132.0582-0.68782.42590.6212-2.13437.3578-0.93891.3505-1.0237-2.16281.64-0.65141.07050.23540.01011.0735-0.32-0.11990.7731-0.22190.886537.784150.270357.1605
141.10370.58040.64972.0457-1.85293.1165-0.26080.998-0.0907-0.84841.08130.51850.3817-0.64333.19351.4596-0.5098-0.55930.99780.22560.567534.880662.162253.0481
153.91173.7379-1.69294.8448-1.31694.34490.030.57141.40860.25131.35042.2109-2.1195-1.0641-0.5240.86560.1142-0.13950.7920.46120.871634.227775.638562.6596
167.0283.7064-5.59415.9646-4.16654.8134-0.27760.427-0.5072-1.74810.1281-0.18280.249-0.3478-0.24790.5845-0.31430.02450.5078-0.06440.518542.135760.442162.1227
171.40842.4738-2.23655.6485-3.40454.7311-0.27460.6457-0.0755-1.32980.4501-0.06680.61750.0912-0.05920.7292-0.1922-0.12080.4497-0.00850.430839.996755.318667.6895
187.1183-0.6504-0.31094.8891-4.73834.72970.02070.2474-0.3716-0.76110.24040.1266-0.25430.3041-0.27860.6683-0.1067-0.08470.58590.04470.509548.582168.092263.0082
196.15993.3763-1.53853.8027-1.25777.5617-0.57410.8935-0.1568-0.76090.36480.06790.12160.090.10810.752-0.0838-0.13960.347-0.03180.473544.024962.063562.2367
205.24543.88824.91054.13294.85455.77330.0661.2602-1.91071.1672-0.2489-1.64591.5592.13680.37271.1183-0.09140.0320.8390.19110.938755.67363.863561.4576
214.6093-7.1014-2.4231.99584.92613.78230.66790.59321.0882-1.41580.49-1.1218-1.52752.8466-1.5740.6466-0.35450.15361.2919-0.53940.801549.523923.982343.3165
225.7621-4.3701-3.75195.8334.65444.17990.9026-0.54731.3743-0.7010.5987-0.2714-1.39031.9991-1.29950.7706-0.0868-0.05861.0323-0.35460.906344.909529.275756.7293
235.1233-2.02751.66942.4872-0.54130.54830.5453-0.84661.1475-0.04250.3079-1.0865-0.40751.1938-0.88220.5066-0.25120.13571.8484-0.38951.115951.738425.694948.1539
244.3312-5.1525-2.35996.54421.80415.14050.81850.04190.0312-0.6350.8197-0.80760.23721.7856-0.93530.62330.0176-0.12551.318-0.24010.622148.560214.283939.534
251.7591.82421.12952.02951.96482.05930.66260.70990.9504-0.4172-0.1373-0.4207-0.45030.828-0.95370.45810.03490.09640.8587-0.04510.360738.17523.163248.8509
262.6242-1.45220.83624.88882.60292.8503-0.48240.7910.4065-0.22990.474-0.1369-1.04040.3715-1.00190.5744-0.13280.07460.44430.02160.385128.509729.554763.0234
274.8318-1.606-3.65661.98611.33472.76720.01930.3015-0.1168-1.39580.70970.1734-0.93311.7068-0.80330.7437-0.0919-0.02190.875-0.2840.594141.630419.556847.276
282.1745-0.2141.69840.19490.22512.20420.39841.63760.6608-0.35060.3949-0.19951.2561-0.4049-0.27980.5145-0.02780.00790.58760.07520.424129.66920.524544.7899
292.89181.391-2.28356.10572.04983.93740.22181.1480.2252-0.26080.10670.30670.4852-0.6578-0.5480.3315-0.0502-0.0660.40070.02440.289623.050822.451559.3533
303.71040.06610.81034.95121.25392.14830.11541.3550.7801-1.37110.7287-0.626-0.58440.2769-0.59250.7722-0.24320.1690.9596-0.12170.722540.464223.485641.7062
313.9785-2.72013.42671.929-2.40513.22020.42391.60420.9737-0.17360.8651-1.3991-0.077-0.4373-0.45030.781-0.18480.22280.97040.00060.842439.062629.593147.0722
320.62231.11190.21452.13690.11770.5776-0.43720.34-0.1985-0.86771.08150.34910.2517-0.5152-0.57351.15810.0417-0.07730.68810.27720.936822.42436.016759.9736
332.2981-3.40330.14695.58951.07892.9494-0.0924-0.65670.66350.5304-0.001-0.28250.21630.26230.12410.5571-0.0798-0.00090.3573-0.06750.531522.53429.644675.47
344.2732-2.3843-5.21722.15522.11397.1473-0.2691-0.42851.04031.32820.0249-0.9547-0.10041.1976-0.4360.6088-0.0641-0.24020.4553-0.07070.375138.516824.178870.7598
357.189-0.50160.3253.20590.74096.1406-0.0826-0.27430.22290.21360.2668-0.25950.27660.3322-0.04340.4907-0.10840.00870.3225-0.05770.398726.454228.819274.6499
367.5831.4399-5.35096.7732-0.29663.8535-0.84650.80240.7516-1.2516-0.11580.8321-0.8135-1.64870.38930.710.0212-0.23060.6852-0.11340.436813.750328.900365.6985
373.5466-0.504-1.93683.59432.23176.9226-0.7212-0.042-0.41290.10680.41490.01140.87260.58590.29740.4553-0.0854-0.05640.2616-0.08090.394530.353518.918464.3571
385.4322.47030.65022.035-1.32613.3449-0.13730.191-0.8909-0.1841-0.22530.06810.1042-0.01250.54210.3849-0.03930.01680.3022-0.05830.311231.453820.327464.7697
396.97090.0463-0.82643.89562.97914.4796-0.1193-0.211-0.73410.59960.0069-0.12290.81170.227-0.05660.6848-0.039-0.01790.2934-0.00940.358424.276816.862268.3015
402.6886-1.4797-1.88511.11980.5674.00390.5938-0.941-0.89811.1139-0.4589-0.40731.439-0.4406-0.21491.16710.0425-0.12350.60590.10940.634227.238711.346676.2327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:9)
2X-RAY DIFFRACTION2(chain A and resid 10:16)
3X-RAY DIFFRACTION3(chain A and resid 17:28)
4X-RAY DIFFRACTION4(chain A and resid 29:41)
5X-RAY DIFFRACTION5(chain A and resid 42:52)
6X-RAY DIFFRACTION6(chain A and resid 53:63)
7X-RAY DIFFRACTION7(chain A and resid 64:71)
8X-RAY DIFFRACTION8(chain A and resid 72:76)
9X-RAY DIFFRACTION9(chain A and resid 77:86)
10X-RAY DIFFRACTION10(chain A and resid 87:102)
11X-RAY DIFFRACTION11(chain A and resid 103:108)
12X-RAY DIFFRACTION12(chain A and resid 109:115)
13X-RAY DIFFRACTION13(chain A and resid 116:121)
14X-RAY DIFFRACTION14(chain A and resid 122:132)
15X-RAY DIFFRACTION15(chain A and resid 133:141)
16X-RAY DIFFRACTION16(chain A and resid 142:147)
17X-RAY DIFFRACTION17(chain A and resid 148:166)
18X-RAY DIFFRACTION18(chain A and resid 167:172)
19X-RAY DIFFRACTION19(chain A and resid 173:196)
20X-RAY DIFFRACTION20(chain A and resid 197:201)
21X-RAY DIFFRACTION21(chain B and resid 1:5)
22X-RAY DIFFRACTION22(chain B and resid 6:17)
23X-RAY DIFFRACTION23(chain B and resid 18:23)
24X-RAY DIFFRACTION24(chain B and resid 24:30)
25X-RAY DIFFRACTION25(chain B and resid 31:37)
26X-RAY DIFFRACTION26(chain B and resid 38:46)
27X-RAY DIFFRACTION27(chain B and resid 47:56)
28X-RAY DIFFRACTION28(chain B and resid 57:63)
29X-RAY DIFFRACTION29(chain B and resid 64:72)
30X-RAY DIFFRACTION30(chain B and resid 73:83)
31X-RAY DIFFRACTION31(chain B and resid 84:89)
32X-RAY DIFFRACTION32(chain B and resid 90:103)
33X-RAY DIFFRACTION33(chain B and resid 104:113)
34X-RAY DIFFRACTION34(chain B and resid 114:121)
35X-RAY DIFFRACTION35(chain B and resid 122:134)
36X-RAY DIFFRACTION36(chain B and resid 135:139)
37X-RAY DIFFRACTION37(chain B and resid 140:152)
38X-RAY DIFFRACTION38(chain B and resid 153:166)
39X-RAY DIFFRACTION39(chain B and resid 167:192)
40X-RAY DIFFRACTION40(chain B and resid 193:200)

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