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- PDB-9m5d: Crystal structure of S. aureus protein A bound to a human single-... -

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Basic information

Entry
Database: PDB / ID: 9m5d
TitleCrystal structure of S. aureus protein A bound to a human single-domain antibody
Components
  • Immunoglobulin G-binding protein A
  • n501
KeywordsIMMUNE SYSTEM / Complex / antibody / S. aureus
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å
AuthorsKong, Y. / Shi, J.L. / Ying, T.L. / Yang, Z.L. / Xu, Q.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82394450 China
CitationJournal: Cell Discov / Year: 2025
Title: A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies.
Authors: Kong, Y. / Shi, J. / Wu, F. / Zhao, T. / Wang, R. / Zhu, X. / Xu, Q. / Song, Y. / Li, Q. / Wang, Y. / Gao, X. / Yang, Y. / Feng, Y. / Wang, Z. / Ge, W. / Wu, Y. / Yang, Z. / Yao, J. / Ying, T.
History
DepositionMar 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: n501
A: n501
H: Immunoglobulin G-binding protein A
B: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)40,0504
Polymers40,0504
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.973, 173.973, 79.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_1ens_2chain "B"
d_2ens_2chain "H"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLUSERSERAB1 - 1201 - 120
d_2ens_1GLUGLUSERSERDA1 - 1201 - 120
d_1ens_2PHEPHELYSLYSBD2803 - 28568 - 61
d_2ens_2PHEPHELYSLYSHC2803 - 28568 - 61

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.458965507321, -0.760669554846, 0.459056087445), (-0.854974938516, 0.518648821588, 0.00461024675134), (-0.24159577314, -0.390365505899, -0.888395325407)-16.1285600831, -20.7260102376, 23.5472585095
2given(0.754169917326, -0.486019861426, 0.441602117409), (-0.535879240944, -0.844179988622, -0.0139135162774), (0.379553915703, -0.226152252056, -0.897103106652)-15.6425656109, -19.1772318028, 24.2781777464

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Components

#1: Antibody n501


Mass: 13179.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 6845.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: spa, SAOUHSC_00069 / Production host: Escherichia coli (E. coli) / References: UniProt: P02976
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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% w/v Polyethylene glycol 3350, 0.2M Magnesium chloride and 0.1M BIS-Tris 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 3.57→123.2 Å / Num. obs: 7538 / % possible obs: 99.63 % / Redundancy: 23.7 % / Biso Wilson estimate: 81.91 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.671 / Net I/av σ(I): 5.65 / Net I/σ(I): 5.4
Reflection shellResolution: 3.57→3.66 Å / Rmerge(I) obs: 3.018 / Num. unique obs: 537 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874phasing
PHENIX1.18.2_3874refinement
DIALSdata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.57→55.02 Å / SU ML: 0.5534 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 376 5.01 %
Rwork0.2331 7135 -
obs0.2351 7511 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.08 Å2
Refinement stepCycle: LAST / Resolution: 3.57→55.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 0 0 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372766
X-RAY DIFFRACTIONf_angle_d0.77283732
X-RAY DIFFRACTIONf_chiral_restr0.048388
X-RAY DIFFRACTIONf_plane_restr0.0064498
X-RAY DIFFRACTIONf_dihedral_angle_d10.8712382
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS1.04531941124
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS1.31180934403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.57-4.090.37711250.29862308X-RAY DIFFRACTION99.71
4.09-5.150.25441110.21622368X-RAY DIFFRACTION99.6
5.15-55.020.23291400.21332459X-RAY DIFFRACTION99.73
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)
10.9841407880460.208099064776-0.1497182219631.006781409490.5716051648161.172000569980.0616126928277-0.0400338167273-0.007313128410420.0297361539506-0.07720886544140.0698365740018-0.157990156141-0.07202920293750.04642703211030.609651165427-0.0722594330393-0.0389285175510.6443301901350.04065413995240.6666643146925.2365546809-43.446257048723.6106500649
21.300880559130.142056394143-0.06295508998321.148776001870.2494666108731.182060097470.06797206730170.2387494815970.113665476954-0.133263402517-0.108801844167-0.0982423897480.0521686570817-0.2915431765430.05469324295610.584537759615-0.0325568691859-0.06358618371150.76582813367-0.03306590409120.7338882683180.42688417585-43.27251829618.8284785647
33.856886874320.0237245983916-0.5900610944053.94150272740.5877942193491.863926980040.03193016473490.03614026466450.206385845353-0.5112558513290.198241379465-0.213098333737-0.1797880509690.236148846508-0.1390790499680.7716261615090.001076294703040.05844610069210.611583212296-0.08040248823260.75891122039837.9833382052-27.103055324815.7512877173
40.5646198041150.2632366620060.9437688410572.55973610879-0.2082362416231.756980209570.300431965514-0.205228132190.1229658126370.236809232127-0.243065665051-0.08531096198140.308727260339-0.109580552893-0.06383919395130.729758795293-0.0471336109199-0.02245070699580.61051543445-0.07136389175770.72230249844941.4524688948-17.450686142731.43824715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'D' and resid 1 through 120)DA1 - 1201 - 120
22(chain 'A' and resid 1 through 120)AB1 - 1201 - 120
33(chain 'H' and resid 2803 through 2856)HC2803 - 28561 - 54
44(chain 'B' and resid 2803 through 2856)BD2803 - 28561 - 54

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