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- PDB-6wvg: human CD53 -

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Basic information

Entry
Database: PDB / ID: 6wvg
Titlehuman CD53
ComponentsGreen fluorescent protein, Leukocyte surface antigen CD53 chimera
KeywordsMEMBRANE PROTEIN / CD53 / tetraspanin-25
Function / homology
Function and homology information


neutrophil degranulation / positive regulation of myoblast fusion / plasma membrane => GO:0005886 / tertiary granule membrane / immunological synapse / specific granule membrane / bioluminescence / generation of precursor metabolites and energy / cell-cell junction / Neutrophil degranulation ...neutrophil degranulation / positive regulation of myoblast fusion / plasma membrane => GO:0005886 / tertiary granule membrane / immunological synapse / specific granule membrane / bioluminescence / generation of precursor metabolites and energy / cell-cell junction / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Leukocyte surface antigen CD53 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, Y. / Liu, S. / Li, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL121718 United States
Other privateForefront of Science Award United States
Other privateMCII 2020-854 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R21 EY028705 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM131008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Citation
Journal: Embo J. / Year: 2020
Title: Open conformation of tetraspanins shapes interaction partner networks on cell membranes.
Authors: Yang, Y. / Liu, X.R. / Greenberg, Z.J. / Zhou, F. / He, P. / Fan, L. / Liu, S. / Shen, G. / Egawa, T. / Gross, M.L. / Schuettpelz, L.G. / Li, W.
#1: Journal: To Be Published
Title: Termini restraining of small membrane proteins enables structure determination at atomic resolution
Authors: Liu, S. / Li, S. / Yang, Y. / Li, W.
History
DepositionMay 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein, Leukocyte surface antigen CD53 chimera
B: Green fluorescent protein, Leukocyte surface antigen CD53 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1659
Polymers102,9402
Non-polymers2,2257
Water32418
1
A: Green fluorescent protein, Leukocyte surface antigen CD53 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1186
Polymers51,4701
Non-polymers1,6475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein, Leukocyte surface antigen CD53 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0483
Polymers51,4701
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.310, 209.770, 73.280
Angle α, β, γ (deg.)90.000, 100.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 151 through 356)
21(chain B and resid 151 through 356)
12(chain A and resid 151 through 354)
22(chain B and resid 151 through 354)
13(chain A and (resid 2 through 142 or resid 366 through 449))
23(chain B and (resid 2 through 142 or resid 366 through 449))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYS(chain A and resid 151 through 356)AA151 - 356149 - 354
211LYSLYSLYSLYS(chain B and resid 151 through 356)BB151 - 356149 - 354
112LYSLYSILEILE(chain A and resid 151 through 354)AA151 - 354149 - 352
212LYSLYSILEILE(chain B and resid 151 through 354)BB151 - 354149 - 352
113SERSERGLUGLU(chain A and (resid 2 through 142 or resid 366 through 449))AA2 - 1422 - 140
123SERSERTHRTHR(chain A and (resid 2 through 142 or resid 366 through 449))AA366 - 449364 - 447
213SERSERGLUGLU(chain B and (resid 2 through 142 or resid 366 through 449))BB2 - 1422 - 140
223SERSERTHRTHR(chain B and (resid 2 through 142 or resid 366 through 449))BB366 - 449364 - 447

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Green fluorescent protein, Leukocyte surface antigen CD53 chimera / Cell surface glycoprotein CD53 / Tetraspanin-25 / Tspan-25


Mass: 51470.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, CD53, MOX44, TSPAN25 / Production host: Komagataella pastoris (fungus) / References: UniProt: P42212, UniProt: P19397
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 6 / Details: 30% PEG 400, 0.1 M KH2PO4, 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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 30225 / % possible obs: 93.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 64.56 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.09 / Rrim(I) all: 0.158 / Χ2: 1.101 / Net I/σ(I): 6.7 / Num. measured all: 84126
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.80.73815480.7220.5280.9121.03997.2
2.95-32.80.6515700.7840.4590.7990.99897.8
3-3.062.80.61415640.8070.4270.750.99297
3.06-3.122.80.48515730.9070.3390.5941.07896.7
3.12-3.192.80.49315580.8360.3460.6051.05597.2
3.19-3.272.70.38315800.9120.2690.4711.10797.3
3.27-3.352.60.36515250.8830.2630.4521.1694.6
3.35-3.442.50.2714490.9220.2040.341.13190.6
3.44-3.542.70.27415420.9150.1970.3391.21193.7
3.54-3.652.90.23115690.9480.160.2821.22597.2
3.65-3.7830.19315750.9690.130.2341.14397.9
3.78-3.942.90.16715650.9670.1150.2041.17797.5
3.94-4.112.90.14515750.9810.10.1771.16296.4
4.11-4.332.80.10515480.9870.0720.1281.16896.3
4.33-4.62.10.0978280.9840.0740.1221.15651.1
4.6-4.962.60.06815160.9930.0480.0841.05792.4
4.96-5.462.70.06515010.9940.0470.081.04193.3
5.46-6.243.10.07815900.9910.0530.0951.01496.5
6.24-7.8630.05615410.9950.0380.0671.03195.7
7.86-502.80.02715080.9980.0190.0331.12890.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.9→35.61 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1232 5.07 %
Rwork0.2157 23069 -
obs0.2183 24301 75.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.79 Å2 / Biso mean: 62.9899 Å2 / Biso min: 24.74 Å2
Refinement stepCycle: final / Resolution: 2.9→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6948 0 107 18 7073
Biso mean--67.73 54.4 -
Num. residues----885
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1235X-RAY DIFFRACTION4.563TORSIONAL
12B1235X-RAY DIFFRACTION4.563TORSIONAL
21A1223X-RAY DIFFRACTION4.563TORSIONAL
22B1223X-RAY DIFFRACTION4.563TORSIONAL
31A1335X-RAY DIFFRACTION4.563TORSIONAL
32B1335X-RAY DIFFRACTION4.563TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.020.3208210.309139341412
3.02-3.150.3309640.28041276134037
3.15-3.320.34911470.27882661280877
3.32-3.530.3431740.26513135330992
3.53-3.80.30011890.23413302349198
3.8-4.180.27861880.2083261344997
4.18-4.790.26521240.19582589271375
4.79-6.020.22481550.18983232338794
6.02-35.610.21561700.19783220339093
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)
11.04950.38720.19544.1951-0.08082.5253-0.0657-0.04840.0110.27440.0998-0.17420.05910.0168-0.03260.15970.01930.02250.21640.00840.22046.3233.01577.262
22.18962.43550.99152.96610.5321.9649-0.3616-0.2867-0.2604-0.299-0.1055-0.2036-0.23630.08440.32240.3127-0.00580.03490.35460.12530.42849.59924.02278.161
30.75150.01490.08254.9459-0.34631.1638-0.06010.06670.0654-0.09280.20870.4828-0.1561-0.2691-0.04440.13510.02270.00070.26990.05890.33820.32356.0977.276
40.8694-0.4406-0.03244.5814-0.18170.24940.13660.08250.2745-0.3867-0.0328-0.4279-0.24450.0765-0.07950.30340.0220.06710.33050.02810.285828.61676.06278.498
53.01230.11730.82157.2443-0.46912.0419-0.1457-0.15990.12730.5525-0.1621-0.8047-0.3409-0.16550.25730.39180.0539-0.0740.2329-0.06550.325316.08112.32783.556
60.25910.10420.04813.8756-1.94061.03540.1557-0.62220.30830.8415-0.10770.8146-0.03240.1057-0.01920.52590.0195-0.15140.3766-0.04250.334210.5191.23388.402
72.4069-0.4736-0.91332.9987-0.01962.15660.0170.0880.21940.2477-0.0022-0.9235-0.37020.35850.04870.2026-0.03860.02330.3387-0.02960.483814.5877.78271.535
82.2402-0.22470.57014.55030.14191.6857-0.0413-0.16540.0189-0.37640.03180.3359-0.0261-0.34350.03360.32540.0366-0.00250.3535-0.0280.216121.094101.715109.859
90.8302-0.64960.54693.18921.6372.78840.16570.0718-0.42960.49560.4720.24260.9437-0.8415-0.61780.7632-0.0378-0.16390.47140.12060.601521.87180.669107.117
101.0083-0.51750.24613.0282-0.85680.85370.04370.1088-0.27920.2713-0.07310.5338-0.14650.0290.02570.43770.0724-0.06020.3478-0.06720.273230.21848.65798.275
110.96090.56670.24033.1547-0.86180.76270.05340.07720.0020.17670.0658-0.20410.16860.0919-0.07190.2706-0.0040.00770.28490.00010.293535.12628.93490.84
121.7689-1.2604-0.34485.64840.0140.6189-0.0119-0.0843-0.2405-0.63760.004-0.15320.0602-0.2565-0.1010.62790.1451-0.07750.4443-0.10520.499421.20992.41498.471
130.9229-0.70390.813.0351-1.13151.1676-0.16970.0913-0.0862-1.21870.13231.1631-0.0584-0.5550.09160.54170.1105-0.10990.6074-0.09680.314814.721103.35499.771
142.8701-0.30430.28373.3952-1.15484.19080.0507-0.0788-0.127-0.70640.1431-0.4104-0.10720.2314-0.110.32270.04830.02870.4127-0.08450.406830.61696.534106.977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:128 )A2 - 128
2X-RAY DIFFRACTION2( CHAIN A AND RESID 129:151 )A129 - 151
3X-RAY DIFFRACTION3( CHAIN A AND RESID 152:249 )A152 - 249
4X-RAY DIFFRACTION4( CHAIN A AND RESID 250:352 )A250 - 352
5X-RAY DIFFRACTION5( CHAIN A AND RESID 353:394 )A353 - 394
6X-RAY DIFFRACTION6( CHAIN A AND RESID 395:417 )A395 - 417
7X-RAY DIFFRACTION7( CHAIN A AND RESID 418:451 )A418 - 451
8X-RAY DIFFRACTION8( CHAIN B AND RESID 2:128 )B2 - 128
9X-RAY DIFFRACTION9( CHAIN B AND RESID 129:151 )B129 - 151
10X-RAY DIFFRACTION10( CHAIN B AND RESID 152:249 )B152 - 249
11X-RAY DIFFRACTION11( CHAIN B AND RESID 250:352 )B250 - 352
12X-RAY DIFFRACTION12( CHAIN B AND RESID 353:394 )B353 - 394
13X-RAY DIFFRACTION13( CHAIN B AND RESID 395:417 )B395 - 417
14X-RAY DIFFRACTION14( CHAIN B AND RESID 418:450 )B418 - 450

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