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- PDB-5vnw: Crystal structure of Nb.b201 bound to human serum albumin -

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Basic information

Entry
Database: PDB / ID: 5vnw
TitleCrystal structure of Nb.b201 bound to human serum albumin
Components
  • Nb.b201
  • Serum albumin
KeywordsTRANSPORT PROTEIN/DE NOVO PROTEIN / nanobody / synthetic protein / llama / camelid / TRANSPORT PROTEIN-DE NOVO PROTEIN complex
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
butanoic acid / LAURIC ACID / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcMahon, C. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Smith Family Foundation United States
National Institutes of Health/Office of the Director1DP5OD021345 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Yeast surface display platform for rapid discovery of conformationally selective nanobodies.
Authors: McMahon, C. / Baier, A.S. / Pascolutti, R. / Wegrecki, M. / Zheng, S. / Ong, J.X. / Erlandson, S.C. / Hilger, D. / Rasmussen, S.G.F. / Ring, A.M. / Manglik, A. / Kruse, A.C.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
C: Nb.b201
D: Nb.b201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,01212
Polymers159,8424
Non-polymers1,1708
Water1,24369
1
A: Serum albumin
D: Nb.b201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6547
Polymers79,9212
Non-polymers7335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
C: Nb.b201
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3585
Polymers79,9212
Non-polymers4373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.338, 72.150, 108.513
Angle α, β, γ (deg.)96.14, 104.60, 104.02
Int Tables number1
Space group name H-MP1

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein Serum albumin /


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768
#2: Antibody Nb.b201


Mass: 13349.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 77 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#6: Chemical ChemComp-BUA / butanoic acid / Butyric acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, Tris(base)/BICINE pH 8.5, PEG 500 MME, PEG 20,0000, sodium chloride, HEPES pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→46.78 Å / Num. obs: 55905 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rsym value: 0.073 / Net I/σ(I): 8.99
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.75 / Num. unique all: 8732 / CC1/2: 0.49 / Rsym value: 1.17 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575:0000)refinement
XDSNov 1, 2016data reduction
XDSNov 1, 2016data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ID7

5id7


Resolution: 2.6→39.6 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.69
RfactorNum. reflection% reflection
Rfree0.2564 3903 3.55 %
Rwork0.2207 --
obs0.2219 55812 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10994 0 77 69 11140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311352
X-RAY DIFFRACTIONf_angle_d0.515343
X-RAY DIFFRACTIONf_dihedral_angle_d22.8714289
X-RAY DIFFRACTIONf_chiral_restr0.1331692
X-RAY DIFFRACTIONf_plane_restr0.0031978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5992-2.63090.35891000.40112760X-RAY DIFFRACTION71
2.6309-2.66420.36291380.41543741X-RAY DIFFRACTION93
2.6642-2.69920.45191370.41263640X-RAY DIFFRACTION95
2.6992-2.73620.42411420.41423872X-RAY DIFFRACTION97
2.7362-2.77530.49661400.43393852X-RAY DIFFRACTION97
2.7753-2.81670.46271380.41123752X-RAY DIFFRACTION98
2.8167-2.86070.41531480.38363960X-RAY DIFFRACTION98
2.8607-2.90760.30811390.35323790X-RAY DIFFRACTION98
2.9076-2.95770.37631450.33933867X-RAY DIFFRACTION97
2.9577-3.01150.35421410.3283865X-RAY DIFFRACTION97
3.0115-3.06940.34431360.33363760X-RAY DIFFRACTION97
3.0694-3.1320.33421460.33423908X-RAY DIFFRACTION97
3.132-3.20010.36721410.32053822X-RAY DIFFRACTION98
3.2001-3.27450.29751400.29933858X-RAY DIFFRACTION98
3.2745-3.35630.3491440.28453834X-RAY DIFFRACTION98
3.3563-3.4470.33271430.26883865X-RAY DIFFRACTION98
3.447-3.54840.29821410.26063831X-RAY DIFFRACTION97
3.5484-3.66290.31181410.2453800X-RAY DIFFRACTION97
3.6629-3.79370.28081400.23733856X-RAY DIFFRACTION97
3.7937-3.94540.25831380.22453768X-RAY DIFFRACTION97
3.9454-4.12480.25211400.19873907X-RAY DIFFRACTION97
4.1248-4.3420.22881410.18243793X-RAY DIFFRACTION97
4.342-4.61370.24411420.16923798X-RAY DIFFRACTION97
4.6137-4.96930.20451400.15813864X-RAY DIFFRACTION97
4.9693-5.46820.20821410.18223870X-RAY DIFFRACTION98
5.4682-6.25680.24791380.19853813X-RAY DIFFRACTION97
6.2568-7.87280.19551430.19463831X-RAY DIFFRACTION96
7.8728-39.64010.16221370.14153785X-RAY DIFFRACTION96
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)
17.11373.2981-0.64086.18131.10814.07810.10830.20650.8011-0.464-0.1280.7527-0.59050.01440.03320.75250.0325-0.02760.6675-0.03630.6549-39.1362101.151758.1398
21.7587-0.0344-1.48112.011.35127.20980.181-0.0398-0.41670.2307-0.055-0.01050.69630.3754-0.1140.7374-0.0422-0.02630.6899-0.10840.7253-41.155784.357570.1784
34.42691.6299-2.91552.9842-0.49335.66870.2863-1.024-0.29620.607-0.0734-0.2480.09041.316-0.23351.0194-0.079-0.15241.0418-0.03270.6261-38.079386.920792.2857
41.27761.02451.45043.39562.57274.6636-0.01710.05870.06970.0504-0.090.24770.7554-0.17020.08921.209-0.13080.05030.69160.12930.6068-61.62168.432576.0212
54.499-1.4166-0.64627.01091.32275.3508-0.23890.0208-0.49931.03110.1891-0.46910.1632.04940.07841.1765-0.0916-0.19211.62130.02730.7967-27.6362-13.77937.2963
63.22530.67631.31012.7705-0.30173.3515-0.0834-0.20380.6470.6941-0.3578-0.1791-1.06610.69680.42531.4461-0.3982-0.01390.9916-0.03390.7238-41.88391.18312.6255
77.4459-0.14521.26851.6855-0.05853.1352-0.06080.8652-0.051-0.4590.1210.0516-0.52860.2463-0.06051.1481-0.1276-0.01760.8272-0.0550.5106-56.1564-8.8205-18.3256
83.44170.9564-0.733.94130.40459.06070.0493-0.51850.3615-0.3366-0.38940.31560.0248-0.61930.31960.89550.0806-0.17030.8413-0.15270.6085-66.22181.54435.2132
90.51751.35321.12336.04526.6448.1049-0.07460.6172-0.0387-0.4432-0.380.2933-0.2696-1.13010.4791.18450.1936-0.25651.4586-0.12140.7217-66.357314.236426.6135
102.40421.55352.3352.51471.47482.4568-1.9905-0.35342.29792.180.4766-2.6569-2.3893-0.8241.56341.0894-0.0706-0.19330.8274-0.13850.8615-55.431632.772755.5424
112.713-3.02490.34013.3616-0.54193.9146-0.0678-0.9675-0.7921.26130.87240.24830.913-0.0768-0.73681.0458-0.231-0.22940.98560.09540.7546-46.983511.917861.6444
126.6176-7.10942.63098.9384-3.36469.12140.1708-0.44580.44210.6143-0.3868-0.0153-0.1135-0.36590.11150.8054-0.28560.07940.8303-0.09970.6476-61.411427.958755.0666
134.6065-5.19984.56687.1897-4.03495.57090.2281-0.36440.831-0.49790.0449-0.2119-0.6408-0.4467-0.25780.86420.035-0.07220.88860.04750.6185-56.15723.855447.5973
143.3721-3.93111.26936.45430.73213.05170.38512.33390.1310.0619-0.4762-0.53550.6140.24150.05080.8988-0.0309-0.09881.0819-0.0190.6942-49.961819.138844.8861
157.857-1.15370.45732.98082.54272.73360.70941.1106-1.4652-0.0052-1.09541.3120.7374-1.27640.28130.8047-0.062-0.17150.9556-0.06680.64-61.961215.77249.4381
167.9312-6.0276-5.62734.79215.29768.41460.3814-0.12950.08990.1253-0.4820.450.1224-1.4070.08350.6291-0.23390.01060.83930.0680.6482-61.311922.357158.4407
175.70985.6561-5.78235.6669-5.79285.91980.34790.4333-0.3074-0.6028-0.79510.17930.9395-0.06230.54971.1858-0.0213-0.01160.7575-0.00160.7206-47.85059.280853.7383
182.7857-2.51110.28086.91716.15488.83430.1042-0.2168-0.1965-0.67550.04530.3563-0.0327-0.6876-0.0740.8017-0.1441-0.05920.660.10240.546-53.426525.485148.8109
198.8774-1.4803-1.40285.13120.5722.04940.27180.78940.796-0.31430.02610.3636-1.11440.5468-0.34341.31150.0978-0.09180.8830.00040.7621-57.150830.454444.3088
204.8567-4.56764.90834.2547-4.59184.90360.15460.71610.40990.8858-1.0531-1.48920.68970.25580.67591.02950.0153-0.16290.80550.03240.717-42.087412.151958.6942
212.3897-0.0246-0.54893.2202-3.6885.4835-0.1930.2276-0.5261-0.5544-0.2367-0.14341.1472-0.43760.36391.6545-0.18280.00461.0983-0.07740.6841-68.771251.067431.3125
224.715-30.95334.7048-4.04144.4131-1.58560.987-2.5387-0.24620.99280.50375.0128-4.37640.43282.1711-0.71460.07791.53230.01220.9908-76.976651.995743.0516
232.5544-1.1378-1.19995.1063-2.89735.6517-0.34850.0873-0.08490.17310.0736-0.06950.7877-0.79410.23531.6362-0.0686-0.11111.0268-0.14610.6755-69.859454.152132.0793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 343 through 584 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 119 )
6X-RAY DIFFRACTION6chain 'B' and (resid 120 through 227 )
7X-RAY DIFFRACTION7chain 'B' and (resid 228 through 376 )
8X-RAY DIFFRACTION8chain 'B' and (resid 377 through 500 )
9X-RAY DIFFRACTION9chain 'B' and (resid 501 through 584 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 7 )
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 17 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 31 )
13X-RAY DIFFRACTION13chain 'C' and (resid 32 through 39 )
14X-RAY DIFFRACTION14chain 'C' and (resid 40 through 51 )
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 72 )
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 82 )
17X-RAY DIFFRACTION17chain 'C' and (resid 83 through 90 )
18X-RAY DIFFRACTION18chain 'C' and (resid 91 through 99 )
19X-RAY DIFFRACTION19chain 'C' and (resid 100 through 111 )
20X-RAY DIFFRACTION20chain 'C' and (resid 112 through 120 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 52 )
22X-RAY DIFFRACTION22chain 'D' and (resid 53 through 59 )
23X-RAY DIFFRACTION23chain 'D' and (resid 60 through 120 )

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