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- PDB-1z68: Crystal Structure Of Human Fibroblast Activation Protein alpha -

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Basic information

Entry
Database: PDB / ID: 1z68
TitleCrystal Structure Of Human Fibroblast Activation Protein alpha
Componentsfibroblast activation protein, alpha subunit
KeywordsLYASE / Seprase / Fibroblast activation protein alpha / FAPalpha / dipeptidylpeptidase / S9b / integral membrane serine protease
Function / homology
Function and homology information


negative regulation of extracellular matrix organization / melanocyte proliferation / peptidase complex / melanocyte apoptotic process / regulation of collagen catabolic process / negative regulation of cell proliferation involved in contact inhibition / prolyl oligopeptidase / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / basal part of cell ...negative regulation of extracellular matrix organization / melanocyte proliferation / peptidase complex / melanocyte apoptotic process / regulation of collagen catabolic process / negative regulation of cell proliferation involved in contact inhibition / prolyl oligopeptidase / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / basal part of cell / regulation of fibrinolysis / dipeptidyl-peptidase activity / lamellipodium membrane / positive regulation of execution phase of apoptosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / endothelial cell migration / serine-type peptidase activity / proteolysis involved in protein catabolic process / ruffle membrane / integrin binding / apical part of cell / lamellipodium / peptidase activity / protease binding / angiogenesis / endopeptidase activity / regulation of cell cycle / cell adhesion / serine-type endopeptidase activity / focal adhesion / cell surface / protein homodimerization activity / proteolysis / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 8 Propeller / Methanol Dehydrogenase; Chain A / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain ...Dipeptidylpeptidase IV, N-terminal domain / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 8 Propeller / Methanol Dehydrogenase; Chain A / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prolyl endopeptidase FAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAertgeerts, K. / Levin, I. / Shi, L. / Prasad, G.S. / Zhang, Y. / Kraus, M.L. / Salakian, S. / Snell, G.P. / Sridhar, V. / Wijnands, R. / Tennant, M.G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein alpha.
Authors: Aertgeerts, K. / Levin, I. / Shi, L. / Snell, G.P. / Jennings, A. / Prasad, G.S. / Zhang, Y. / Kraus, M.L. / Salakian, S. / Sridhar, V. / Wijnands, R. / Tennant, M.G.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_validate_chiral.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fibroblast activation protein, alpha subunit
B: fibroblast activation protein, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,17011
Polymers166,5702
Non-polymers2,6009
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint21 kcal/mol
Surface area59100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.295, 152.580, 214.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fibroblast activation protein, alpha subunit


Mass: 83284.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastbacHTb / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 cells
References: UniProt: Q12884, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 6 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.6 / Details: pH 7.6, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 28, 2002 / Details: SINGLE CRYSTAL, SINGLE MIRROR
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 70612 / Redundancy: 3.4 % / Rsym value: 0.095 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.507 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R9M

1r9m


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / SU B: 13.411 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28257 3558 5 %RANDOM
Rwork0.22313 ---
obs0.22619 66976 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--6 Å20 Å2
3----7.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11778 0 168 628 12574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.94816806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15151436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.21776
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029491
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.26485
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2658
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.14327173
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.929311635
X-RAY DIFFRACTIONr_scbond_it1.17125172
X-RAY DIFFRACTIONr_scangle_it1.85735170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.413 244
Rwork0.342 4381
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)
10.9227-0.0350.19230.9407-0.40362.06850.0006-0.1637-0.00730.3957-0.062-0.12140.01940.25750.06140.36390.0191-0.08280.28010.14320.256537.97290.756269.4363
21.05770.29060.04150.911-0.41631.39620.08320.1185-0.1318-0.1006-0.0180.0470.36580.0091-0.06520.09360.0703-0.00450.05640.02420.211124.989713.086215.7584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 531 - 15
2X-RAY DIFFRACTION1AA54 - 22916 - 191
3X-RAY DIFFRACTION1AA230 - 259192 - 221
4X-RAY DIFFRACTION1AA260 - 492222 - 454
5X-RAY DIFFRACTION1AA493 - 757455 - 719
6X-RAY DIFFRACTION1AC4901
7X-RAY DIFFRACTION1AD9201 - 9202
8X-RAY DIFFRACTION1AE2271 - 2272
9X-RAY DIFFRACTION2BB39 - 531 - 15
10X-RAY DIFFRACTION2BB54 - 22916 - 191
11X-RAY DIFFRACTION2BB230 - 259192 - 221
12X-RAY DIFFRACTION2BB260 - 492222 - 454
13X-RAY DIFFRACTION2BB493 - 757455 - 719
14X-RAY DIFFRACTION2BG4901
15X-RAY DIFFRACTION2BH9201 - 9202
16X-RAY DIFFRACTION2BJ3141
17X-RAY DIFFRACTION2BK6791

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