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- PDB-6m58: Crystal structure of a complex between human serum albumin and th... -

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Basic information

Entry
Database: PDB / ID: 6m58
TitleCrystal structure of a complex between human serum albumin and the antibody Fab SL335
Components
  • Heavy chain of the SL335 antibody fab
  • Light chain of the SL335 antibody Fab
  • Serum albumin
KeywordsIMMUNE SYSTEM / SERUM ALBUMIN / ANTI-ALBUMIN / ANTIBODY FAB
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / cellular response to starvation / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis of serum albumin recognition by SL335, an antibody Fab extending the serum half-life of protein therapeutics.
Authors: Cho, S.Y. / Han, J. / Cha, S.H. / Yoon, S.I.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.3Oct 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: Serum albumin
H: Heavy chain of the SL335 antibody fab
L: Light chain of the SL335 antibody Fab
B: Serum albumin
C: Heavy chain of the SL335 antibody fab
D: Light chain of the SL335 antibody Fab


Theoretical massNumber of molelcules
Total (without water)228,3636
Polymers228,3636
Non-polymers00
Water54030
1
A: Serum albumin
H: Heavy chain of the SL335 antibody fab
L: Light chain of the SL335 antibody Fab


Theoretical massNumber of molelcules
Total (without water)114,1813
Polymers114,1813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-29 kcal/mol
Surface area43260 Å2
MethodPISA
2
B: Serum albumin
C: Heavy chain of the SL335 antibody fab
D: Light chain of the SL335 antibody Fab


Theoretical massNumber of molelcules
Total (without water)114,1813
Polymers114,1813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-29 kcal/mol
Surface area41930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.607, 103.931, 161.082
Angle α, β, γ (deg.)90.000, 93.083, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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: Homo sapiens (human) / References: UniProt: P02768
#2: Antibody Heavy chain of the SL335 antibody fab


Mass: 24278.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Antibody Light chain of the SL335 antibody Fab


Mass: 23331.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Tris, pH 8.5, glycerol, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 47902 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.4
Reflection shellResolution: 2.95→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2445 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2-3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CSZ, 1AO6

5csz

1ao6


Resolution: 2.95→30 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / Phase error: 25.1875
RfactorNum. reflection% reflection
Rfree0.242 2296 -
Rwork0.193 --
obs-44707 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 62.4 Å2
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14723 0 0 30 14753
LS refinement shellResolution: 2.95→3.0141 Å
RfactorNum. reflection% reflection
Rfree0.3531 134 -
Rwork0.2813 2793 -
obs--99 %
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)
10.5609-0.1969-0.14181.29250.03741.4678-0.08660.0668-0.1994-0.041-0.11040.05660.4257-0.17550.14860.5783-0.0202-0.00220.2693-0.01870.54354.553319.098844.0874
21.9557-1.060.28542.0803-0.73121.6395-0.1728-0.1795-0.03550.24060.1808-0.0371-0.08530.1162-0.02670.55820.016-0.05260.1775-0.00740.4627.52433.66569.3257
32.6029-1.2653-1.55632.48871.14130.8835-0.06450.1105-0.29190.2551-0.043-0.29430.25890.11880.10390.87520.0796-0.03780.33480.04580.616824.23944.573864.3571
42.6334-1.2853-0.24693.63640.25590.6658-0.1351-0.01930.26020.3250.0182-0.2094-0.13340.02640.09980.4856-0.009-0.04370.17520.00260.4012-10.270256.800967.8059
53.2352-1.48560.12973.73380.97620.9397-0.0538-0.1328-0.04380.3344-0.1469-0.05450.0276-0.01110.16850.5216-0.037-0.04630.1664-0.01530.3892-13.398355.860467.6874
64.54180.217-0.26160.97631.37611.91850.0183-0.00780.26280.146-0.2640.1520.0216-0.52540.17160.4832-0.0009-0.01920.3102-0.07910.5558-39.991467.100867.3983
76.6132.75962.03571.49720.36091.31440.2322-1.03580.3052-0.0029-0.15380.46810.2344-0.9118-0.05630.5246-0.0870.02070.5526-0.07780.7445-47.165965.362472.1822
81.5753-1.9153-0.54242.37070.3632.95860.09320.7639-0.5681-0.071-0.28160.54960.4663-0.41440.06880.572-0.0006-0.09990.3453-0.09510.5343-26.055845.314847.7466
96.7033-0.82750.79450.1652-0.35771.32030.24750.9535-0.58180.2947-0.27510.09060.29190.2032-0.02030.63480.0901-0.09610.0616-0.08490.5218-16.267443.767550.5868
101.8734-0.40340.52650.2962-0.04550.1646-0.0353-0.4766-0.74280.3840.00110.31170.4440.01080.05620.6196-0.0788-0.00990.2491-0.06050.6941-21.99739.810360.9987
118.19520.6831-0.92170.0425-0.07580.09850.39541.0301-0.64510.0521-0.10150.42030.2272-0.12530.00510.63460.0193-0.09950.321-0.15370.7294-18.505737.753348.4346
120.7605-0.3013-0.55162.21090.60941.4687-0.01780.0573-0.5336-0.0962-0.31740.54670.1686-0.2892-0.2850.7290.0001-0.09820.1518-0.08090.5819-27.188542.414155.7003
133.2263-1.78810.42892.12540.79230.95390.11720.27180.4175-0.0226-0.24020.26970.0236-0.34730.15910.5525-0.03920.03190.2898-0.04230.6176-34.209358.472655.9311
143.67420.00120.41247.6683.42225.8172-0.0879-0.1267-0.0120.2582-0.2090.57690.0547-0.55570.36480.3705-0.0251-0.04560.4905-0.21610.6523-45.566662.23954.2801
153.5461-1.6863-1.55278.38532.65595.7205-0.43760.67841.0416-1.2864-0.29480.8358-0.6521-1.18060.370.72840.0975-0.39730.3383-0.13831.0227-47.585273.425346.0576
164.10931.3742-0.13351.89730.31394.3893-0.15060.0831-0.43290.33150.11910.251-0.2849-0.5550.05030.4925-0.0317-0.1030.3528-0.11880.5056-40.922358.576755.3915
174.3978-2.4227-1.29551.60181.84784.958-0.1174-0.18931.3744-0.07390.13430.3415-1.47960.07970.08570.60470.2163-0.15910.4533-0.13791.1194-45.499677.123455.8971
182.7842-1.8372-0.58868.14032.43622.8346-0.17610.55270.5187-0.64490.02061.0761-0.6938-0.19310.30160.5940.1238-0.23880.5733-0.06670.9275-50.921272.873648.9005
192.8361-1.301-0.57354.67522.06633.82770.20120.40220.148-0.5737-0.00740.9955-0.4549-0.6920.28710.3870.2166-0.40570.7293-0.1721.2368-54.257464.782347.1847
202.0462-0.0951-0.62791.53680.38782.6631-0.02670.74430.0014-0.212-0.00930.1327-0.1007-0.57510.02290.39360.0145-0.10320.6680.02750.4675-28.665260.617632.5598
211.8219-0.567-1.87670.63030.21072.27390.07780.34120.30430.06740.016-0.1329-0.1251-0.2237-0.12290.46360.051-0.05540.30040.07090.4661-11.025868.078833.8338
222.4184-1.8328-0.39444.06530.55412.50260.37290.35770.6375-0.5418-0.3582-0.4741-0.43350.2771-0.04020.57450.01070.06040.47540.29710.79668.089577.137716.7236
231.8297-1.43110.04841.73890.72211.71920.27890.36310.7026-0.2792-0.2546-0.1676-0.2675-0.1818-0.00760.72870.14150.08780.49430.21980.8039-18.690996.205523.4779
243.2856-1.8263-0.2674.8850.75662.38530.11630.4869-0.0244-0.3671-0.33940.0030.0489-0.06470.27210.40520.0621-0.00880.36090.06320.520618.447843.66117.1497
256.3260.45320.19180.81651.87145.13080.2037-0.28440.4781-0.1839-0.2020.0799-0.15530.1007-0.26360.3856-0.0122-0.07470.35570.05460.39715.167850.307226.8933
263.063-0.74360.188641.32451.82920.08170.51420.48570.025-0.004-0.2924-0.3413-0.1196-0.12760.3761-0.0207-0.01440.30910.12570.406118.474245.075722.7759
272.1601-1.34270.13773.6151.81941.07830.09320.2457-0.0479-0.4282-0.1107-0.30380.0403-0.01270.01470.50420.01180.11390.37780.07730.309919.83127.345213.1139
285.93462.42611.15584.2861.63672.6545-0.09450.6154-0.3396-0.9909-0.2106-0.40630.0996-0.3681-0.01960.69910.06180.04220.4791-0.06160.487519.897518.19326.5181
295.0051.8904-0.46663.52311.45751.00160.021-0.2614-0.4565-0.3926-0.0715-0.35470.8432-0.82730.05990.64270.00520.10560.65190.07070.384216.512918.045611.4253
304.1071-0.6236-1.76645.32322.28266.8380.3451.2316-0.5727-0.58970.6117-0.71120.60640.4567-0.71910.95960.1118-0.04560.7979-0.26090.653312.18729.5477-2.7907
316.89850.46121.27743.2081.12425.3188-0.15851.67090.1145-1.34030.656-0.23-0.62480.7717-0.48310.7437-0.010.13030.7963-0.05320.588523.967518.44621.4185
323.1604-2.2108-2.39165.06560.43073.70890.09190.4984-0.84070.3757-0.12690.84720.8183-1.04940.04180.5408-0.00280.05420.4756-0.13990.5758-5.598431.049223.871
333.3964-0.0245-1.14614.9721-2.01951.52690.16610.8354-0.074-0.30390.01230.936-0.0426-0.1714-0.08430.41480.0653-0.11520.5244-0.05520.4174-2.65541.274820.2659
344.8194-1.3732-2.29917.70834.59063.29190.1320.5799-0.38130.496-0.24150.7950.5821-0.0829-0.09290.3507-0.0306-0.05540.4359-0.0810.6192-9.747640.902124.9063
354.4057-0.7144-0.13164.0164-0.14941.5856-0.08971.0297-0.933-0.561-0.46480.29920.2177-0.3010.42080.4558-0.0133-0.06410.7977-0.24270.563-3.954434.506716.1659
364.2619-1.13280.37295.15844.47546.2337-0.0675-0.2569-0.18690.4720.7658-0.58470.1868-0.3402-0.55490.4321-0.0314-0.02050.40250.1590.43914.728743.929929.5815
370.1218-0.57240.09856.12881.11720.75480.10310.1195-0.85850.211-0.10560.97250.5168-0.33020.30140.7773-0.0940.02190.6757-0.45860.9749-5.38417.941913.6727
382.1025-0.87410.47555.07431.40743.37160.46890.2425-0.9688-0.2884-0.2586-0.39680.8069-0.1231-0.24870.7346-0.0004-0.06090.4747-0.02890.834812.79386.366113.1715
393.73272.21980.14482.06781.76863.8225-0.4843-0.1842-1.19110.1118-0.2683-0.46941.1496-0.18130.4750.9778-0.16610.22050.519-0.0111.022614.08054.675922.4303
404.5312-1.73310.0963.2717-2.251.888-0.24240.65640.7517-0.217-0.41120.3208-0.5751-0.25080.60390.7249-0.1976-0.13040.6438-0.05880.69270.979519.54829.5039
413.41011.79730.56643.8170.65212.2577-0.2675-0.5102-2.03670.27120.0983-0.04331.0936-0.01860.13221.1076-0.0180.07180.4487-0.11721.108712.31070.663216.5834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 227 )A5 - 227
2X-RAY DIFFRACTION2chain 'A' and (resid 228 through 398 )A228 - 398
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 582 )A399 - 582
4X-RAY DIFFRACTION4chain 'H' and (resid 2 through 72 )H2 - 72
5X-RAY DIFFRACTION5chain 'H' and (resid 73 through 111 )H73 - 111
6X-RAY DIFFRACTION6chain 'H' and (resid 112 through 182 )H112 - 182
7X-RAY DIFFRACTION7chain 'H' and (resid 183 through 221 )H183 - 221
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 18 )L1 - 18
9X-RAY DIFFRACTION9chain 'L' and (resid 19 through 38 )L19 - 38
10X-RAY DIFFRACTION10chain 'L' and (resid 39 through 61 )L39 - 61
11X-RAY DIFFRACTION11chain 'L' and (resid 62 through 75 )L62 - 75
12X-RAY DIFFRACTION12chain 'L' and (resid 76 through 90 )L76 - 90
13X-RAY DIFFRACTION13chain 'L' and (resid 91 through 128 )L91 - 128
14X-RAY DIFFRACTION14chain 'L' and (resid 129 through 143 )L129 - 143
15X-RAY DIFFRACTION15chain 'L' and (resid 144 through 155 )L144 - 155
16X-RAY DIFFRACTION16chain 'L' and (resid 156 through 174 )L156 - 174
17X-RAY DIFFRACTION17chain 'L' and (resid 175 through 187 )L175 - 187
18X-RAY DIFFRACTION18chain 'L' and (resid 188 through 198 )L188 - 198
19X-RAY DIFFRACTION19chain 'L' and (resid 199 through 210 )L199 - 210
20X-RAY DIFFRACTION20chain 'B' and (resid 5 through 130 )B5 - 130
21X-RAY DIFFRACTION21chain 'B' and (resid 131 through 291 )B131 - 291
22X-RAY DIFFRACTION22chain 'B' and (resid 292 through 398 )B292 - 398
23X-RAY DIFFRACTION23chain 'B' and (resid 399 through 582 )B399 - 582
24X-RAY DIFFRACTION24chain 'C' and (resid 2 through 44 )C2 - 44
25X-RAY DIFFRACTION25chain 'C' and (resid 45 through 59 )C45 - 59
26X-RAY DIFFRACTION26chain 'C' and (resid 60 through 100 )C60 - 100B
27X-RAY DIFFRACTION27chain 'C' and (resid 101 through 142 )C100C - 142
28X-RAY DIFFRACTION28chain 'C' and (resid 143 through 164 )C143 - 164
29X-RAY DIFFRACTION29chain 'C' and (resid 165 through 184 )C165 - 184
30X-RAY DIFFRACTION30chain 'C' and (resid 185 through 200 )C185 - 200
31X-RAY DIFFRACTION31chain 'C' and (resid 201 through 220 )C201 - 220
32X-RAY DIFFRACTION32chain 'D' and (resid 1 through 18 )D1 - 18
33X-RAY DIFFRACTION33chain 'D' and (resid 19 through 61 )D19 - 61
34X-RAY DIFFRACTION34chain 'D' and (resid 62 through 75 )D62 - 75
35X-RAY DIFFRACTION35chain 'D' and (resid 76 through 90 )D76 - 90
36X-RAY DIFFRACTION36chain 'D' and (resid 91 through 102 )D91 - 102
37X-RAY DIFFRACTION37chain 'D' and (resid 103 through 113 )D103 - 113
38X-RAY DIFFRACTION38chain 'D' and (resid 114 through 150 )D114 - 150
39X-RAY DIFFRACTION39chain 'D' and (resid 151 through 163 )D151 - 163
40X-RAY DIFFRACTION40chain 'D' and (resid 164 through 174 )D164 - 174
41X-RAY DIFFRACTION41chain 'D' and (resid 175 through 210 )D175 - 210

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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