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- PDB-7c94: Crystal structure of the anti-human podoplanin antibody Fab fragm... -

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Basic information

Entry
Database: PDB / ID: 7c94
TitleCrystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide
Components
  • Heavy chain of Fab fragment
  • Light chain of Fab fragment
  • Peptide from Podoplanin
KeywordsIMMUNE SYSTEM / human podoplanin / monoclonal antibody / glycopeptide
Function / homology
Function and homology information


regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis ...regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / wound healing, spreading of cells / anchoring junction / microvillus membrane / lamellipodium membrane / lymph node development / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / Rho protein signal transduction / ruffle / lung development / cell projection / filopodium / platelet activation / ruffle membrane / cell junction / cell migration / regulation of cell shape / lamellipodium / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / cell adhesion / positive regulation of cell migration / apical plasma membrane / membrane raft / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
: / Podoplanin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Podoplanin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsSuzuki, K. / Nakamura, S. / Ogasawara, S. / Naruchi, K. / Shimabukuro, J. / Tukahara, N. / Kaneko, M.K. / Kato, Y. / Murata, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.
Authors: Ogasawara, S. / Suzuki, K. / Naruchi, K. / Nakamura, S. / Shimabukuro, J. / Tsukahara, N. / Kaneko, M.K. / Kato, Y. / Murata, T.
History
DepositionJun 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of Fab fragment
B: Heavy chain of Fab fragment
C: Peptide from Podoplanin
D: Light chain of Fab fragment
E: Heavy chain of Fab fragment
F: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,53919
Polymers100,5826
Non-polymers2,95613
Water37821
1
A: Light chain of Fab fragment
B: Heavy chain of Fab fragment
C: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7209
Polymers50,2913
Non-polymers1,4296
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-29 kcal/mol
Surface area20230 Å2
MethodPISA
2
D: Light chain of Fab fragment
E: Heavy chain of Fab fragment
F: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,81810
Polymers50,2913
Non-polymers1,5277
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-38 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 42.960, 221.080
Angle α, β, γ (deg.)90.000, 91.366, 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

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Antibody , 2 types, 4 molecules ADBE

#1: Antibody Light chain of Fab fragment


Mass: 24260.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Heavy chain of Fab fragment


Mass: 24145.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein/peptide / Sugars , 2 types, 4 molecules CF

#3: Protein/peptide Peptide from Podoplanin / Aggrus / Glycoprotein 36 / Gp36 / PA2.26 antigen / T1-alpha / T1A


Mass: 1885.144 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: We synthesized the binding epitope region of the Fab fragment that includes the peptide (-L67VATSVNSV-T76-GIRIEDLP84-) possessing a disialyl-core-1 O-glycan at Ther76.
Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YL7
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 965.858 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3[DNeup5Aca2-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-3/a3-b1_a6-d2_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 32 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5, 0.2M magnesium Acetate, 25% v/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.84→44.2 Å / Num. obs: 19390 / % possible obs: 98.8 % / Redundancy: 5.852 % / Biso Wilson estimate: 47.21 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.184 / Rrim(I) all: 0.202 / Χ2: 0.913 / Net I/σ(I): 7.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.84-3.024.7080.6572.0431290.7480.73996.1
3.02-3.226.3340.4713.5327990.8840.51399.1
3.22-3.486.2790.3364.9227200.9310.36699.3
3.48-3.816.1940.2277.1925310.9780.24899.4
3.81-4.256.0610.1569.8322610.9870.1799.5
4.25-4.95.8530.11212.9320100.990.12299.1
4.9-5.995.440.11312.0317620.9890.12599.8
5.99-8.396.2530.10813.5413610.9920.11799.9
8.39-44.25.7370.07117.578170.9970.07797.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4J

1a4j


Resolution: 2.84→44.2 Å / SU ML: 0.4193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0776 / Stereochemistry target values: CDL v1.2 / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflection
Rfree0.2553 1940 10.02 %
Rwork0.2195 33139 -
obs0.2231 19390 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.24 Å2
Refinement stepCycle: LAST / Resolution: 2.84→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 62 21 7077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297220
X-RAY DIFFRACTIONf_angle_d0.74049843
X-RAY DIFFRACTIONf_chiral_restr0.04461119
X-RAY DIFFRACTIONf_plane_restr0.00421231
X-RAY DIFFRACTIONf_dihedral_angle_d15.35694251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.37871250.34151193X-RAY DIFFRACTION89.48
2.88-2.920.36681580.34951229X-RAY DIFFRACTION97.74
2.92-2.960.36331290.31721213X-RAY DIFFRACTION97.96
2.96-3.010.29031570.28961289X-RAY DIFFRACTION98.37
3.01-3.050.35491480.29651291X-RAY DIFFRACTION97.03
3.05-3.10.33121370.2911263X-RAY DIFFRACTION97.63
3.1-3.160.28081310.28411231X-RAY DIFFRACTION100
3.16-3.210.28891530.25521322X-RAY DIFFRACTION99.86
3.21-3.280.29811440.24151265X-RAY DIFFRACTION99.16
3.28-3.340.28931450.25031278X-RAY DIFFRACTION98.82
3.34-3.410.25661330.22191283X-RAY DIFFRACTION99.93
3.41-3.490.29321360.24611261X-RAY DIFFRACTION99.57
3.49-3.580.2421650.21971419X-RAY DIFFRACTION99.31
3.58-3.680.28121160.22771171X-RAY DIFFRACTION99.31
3.68-3.790.24261450.20851306X-RAY DIFFRACTION99.66
3.79-3.910.2151410.19541308X-RAY DIFFRACTION99.25
3.91-4.050.28461560.20521259X-RAY DIFFRACTION99.44
4.05-4.210.26271190.19921287X-RAY DIFFRACTION99.79
4.21-4.40.23251400.18461308X-RAY DIFFRACTION99.18
4.4-4.630.2241380.1611250X-RAY DIFFRACTION99.78
4.63-4.920.17871490.17621265X-RAY DIFFRACTION99.44
4.92-5.30.23341480.19151312X-RAY DIFFRACTION99.66
5.3-5.840.21351530.20021240X-RAY DIFFRACTION99.71
5.84-6.680.24911550.21621298X-RAY DIFFRACTION99.73
6.68-8.40.20751340.20021314X-RAY DIFFRACTION99.86
8.4-44.20.24881350.21081284X-RAY DIFFRACTION98.34
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)
10.1112968559190.0666566227043-0.02632905208850.003499725809530.05968679877050.0114018343002-0.463279104438-0.522645365254-0.4405615699240.0525219378090.214982305175-0.1385687463240.543493206004-0.0758835415309-0.006633125968340.4109629366-0.001220027937420.01397266541540.5207161254810.01340130617360.321761405484-14.73644607152.29157274858-99.7412884404
21.55373679576-0.0755769880218-0.253639636881.25564842189-0.7907331720811.073739856110.02120531929410.339546674966-0.0947903519063-0.259807072263-0.0370817169031-0.1654981246710.02258584004010.227160156685-1.22185587131E-50.3151995361030.00444736662153-0.01958854279270.406952538824-0.01268978037860.403258481932-17.566077265212.5399893971-104.878523493
30.894907961705-0.745701540258-0.1448645671070.165191445071-0.6635307218282.04273221111-0.2616753585710.0273816513477-0.01239350362490.07354522937760.02506939997550.0949405858706-0.06106160556460.10495931523-0.008187427931870.382450134978-0.0168496383680.0121830848660.281204170571-0.008596197914280.361717634705-13.28472269366.2341203943-95.6431064913
41.28527259835-0.493383128155-1.147781782520.8857790202791.069390191941.493989999590.1223348777470.2955386252990.02127863443230.1755606661430.01358036856020.0940478261956-0.0802026060928-0.04212301337164.53235337934E-50.32022216383-0.0213298273951-0.04220465382830.3303710138680.0241077970650.334922773724-11.3771315417-7.63821742392-73.1486115759
51.787948623010.705125549611-1.03122065382.01119166936-0.698103004740.895906525108-0.2364392395680.0457346587065-0.367287646580.17679154176-0.114893679019-0.2072132356460.471451068038-0.293373204037-0.003029076068530.3483768951450.0516771183405-0.05492182776070.348957627636-0.04364852509580.481678449507-13.4031092253-15.4811243795-67.9841794952
62.43655145503-0.366012994439-0.9728410997461.632843027530.7571306920141.57468223541-0.120312473351-0.170639356308-0.04173639838830.07477597769690.1246896268450.179751506842-0.0662118256264-0.180549620139-9.93345077718E-60.3340296764080.0183490893302-0.05106216744220.3773693261150.03276520167590.323367833119-29.163117976422.860233623-87.6733090156
70.783357207173-0.3816191032490.2792086388110.439385282335-0.4870708852811.53160154263-0.01437944867480.06829409721990.04229154607060.07708171370490.0536334633261-0.0184868505726-0.0330232632270.159881223253-9.02998803338E-60.34546845613-0.0273420181487-0.01208722806550.265585031742-0.02133828874910.384613316268-9.904114240455.18924786063-68.9697345737
84.370247914951.756637774390.9961631439992.02484102194-0.1028656896430.429309657547-1.082941340391.212363539270.0834236579341-0.778743417669-0.3999507688180.381571446750.672803198391-0.102075774139-0.2406148030051.38915075433-0.1895170192380.4368375225640.630169385313-0.0235127732117-0.00650114084983-36.542380659625.8641569971-103.772286873
90.4191582466460.04632263852980.2758248507770.7822463028930.9117372754860.872654456978-0.0453772885763-0.514163866854-0.3837939729110.142658319307-0.2411401582330.1564482837410.1850968646370.205895006078-4.02385498763E-50.5209793603480.103479900030.1106038326510.5808646555410.04925597688580.6852256209281.7674723137-0.440656644796-5.80753702975
100.8355556230380.4692864837320.1871484265580.749022931038-0.5198034080171.087973241740.0167003786254-0.2268862424310.05851064970650.201107798123-0.0936333470440.0538335602266-0.101042108774-0.009928220790274.54447296874E-60.3318032969820.05454135476520.01147231772580.340502832701-0.04594296539120.3499423287488.339567146081.88586728171-20.5140605544
111.04058847241-0.194711624850.754327166812.30508980446-1.078044460051.64932640038-0.0291126590324-0.09868449163170.2522409469410.101882459966-0.1063698470690.0634268356027-0.07545494733040.0179055005724-4.59709387297E-70.340472746288-0.0103752044854-0.008435096803010.317901619661-0.05567575527480.3549130348289.1989948629316.0853915737-38.0584692013
120.660573119911-0.3190262826820.8075790528660.367458693255-0.554688797870.8584262399750.634992805640.662957037862-0.770689164191-0.123146350665-0.08202863636750.2310870868440.7132382314290.3733805719650.006424500252220.472393439341-0.040047038103-0.05343296504280.4581292121850.138154219880.38249537567-2.9780197411-19.3353365307-29.4226898456
131.833743697250.246420810149-0.1172932173280.8728716727360.7139812511672.1733948966-0.1148606039150.01708003800090.101487434821-0.0368181371515-0.06255184807940.08800149267490.0723152121828-0.1388371924541.73118065134E-60.3565314694740.02104191674060.01714538389050.4668645999110.02513165707940.485816804616-8.25778064571-17.8722936595-21.0965302116
14-0.163332959772-0.03099352590390.06101483264290.992265633786-0.2037011345743.51696267647-0.103264944319-0.0822711245299-0.04455165561280.01044781738910.123465084956-0.04061064486930.213720655564-0.528959160849-0.00232313610920.09734149738350.0983619200539-0.0144822710340.3305432518790.0286874394890.4468559589853.68750233999-5.91187178381-30.5701791491
151.201155334640.901385206265-0.01785829058431.916617231180.188136410032.123828205650.107054194526-0.2670398545080.01563339187030.0639702558888-0.01050214571930.00916444692669-0.1527877649650.105941615461-8.69350843315E-50.317805063301-0.01458661119-0.0129075257280.2836931185270.009407764190640.29603112895815.35148157262.30455938624-45.7457077247
161.762056280940.4837657465620.08110032126730.4100453168640.676193606061.45026428519-0.5143695060830.178959406853-0.0212795890124-0.173331351616-0.5664649675620.1647510906560.0348994774772-0.374957603345-0.6961511080690.519506109066-0.0470366988311-0.07053232848590.6558225678020.1120280410971.26412233756-15.2241505696-20.8252665889-6.18772177012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 180 )
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 220 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 225 )
8X-RAY DIFFRACTION8chain 'C' and (resid 75 through 81 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 38 )
10X-RAY DIFFRACTION10chain 'D' and (resid 39 through 161 )
11X-RAY DIFFRACTION11chain 'D' and (resid 162 through 219 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 17 )
13X-RAY DIFFRACTION13chain 'E' and (resid 18 through 98 )
14X-RAY DIFFRACTION14chain 'E' and (resid 99 through 143 )
15X-RAY DIFFRACTION15chain 'E' and (resid 144 through 225 )
16X-RAY DIFFRACTION16chain 'F' and (resid 75 through 81 )

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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