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- PDB-6n9t: Structure of a peptide-based photo-affinity cross-linker with Her... -

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Basic information

Entry
Database: PDB / ID: 6n9t
TitleStructure of a peptide-based photo-affinity cross-linker with Herceptin Fc
Components
  • Immunoglobulin G1 FC
  • Photo-affinity peptide
KeywordsIMMUNE SYSTEM / Crosslinking / antibody / photo-reactive
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.576 Å
AuthorsSadowsky, J. / Ultsch, M. / Vance, N. / Wang, W.
CitationJournal: Bioconjug. Chem. / Year: 2019
Title: Development, Optimization, and Structural Characterization of an Efficient Peptide-Based Photoaffinity Cross-Linking Reaction for Generation of Homogeneous Conjugates from Wild-Type Antibodies.
Authors: Vance, N. / Zacharias, N. / Ultsch, M. / Li, G. / Fourie, A. / Liu, P. / LaFrance-Vanasse, J. / Ernst, J.A. / Sandoval, W. / Kozak, K.R. / Phillips, G. / Wang, W. / Sadowsky, J.
History
DepositionDec 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G1 FC
E: Photo-affinity peptide
B: Immunoglobulin G1 FC
F: Photo-affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3716
Polymers53,8514
Non-polymers2,5202
Water3,063170
1
A: Immunoglobulin G1 FC
E: Photo-affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1863
Polymers26,9252
Non-polymers1,2601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint16 kcal/mol
Surface area12060 Å2
MethodPISA
2
B: Immunoglobulin G1 FC
F: Photo-affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1863
Polymers26,9252
Non-polymers1,2601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint17 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.112, 60.850, 68.167
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Immunoglobulin G1 FC


Mass: 25239.570 Da / Num. of mol.: 2 / Fragment: residues 249-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MZV7
#2: Protein/peptide Photo-affinity peptide


Mass: 1685.898 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 100mM sodium acetate pH=5.6, 12%(w/v) PEG 1000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.576→50 Å / Num. obs: 31910 / % possible obs: 100 % / Redundancy: 3.4 % / Net I/σ(I): 8.6
Reflection shellResolution: 2.576→2.585 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.576→44.224 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 31.54
RfactorNum. reflection% reflection
Rfree0.2651 1650 5.17 %
Rwork0.2289 --
obs0.2309 31910 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.576→44.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 170 170 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033851
X-RAY DIFFRACTIONf_angle_d0.5855234
X-RAY DIFFRACTIONf_dihedral_angle_d16.0542313
X-RAY DIFFRACTIONf_chiral_restr0.042596
X-RAY DIFFRACTIONf_plane_restr0.004643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5759-2.65170.4291410.34122517X-RAY DIFFRACTION97
2.6517-2.73730.4681190.30892515X-RAY DIFFRACTION97
2.7373-2.83510.36811180.2722557X-RAY DIFFRACTION98
2.8351-2.94860.34631550.26912510X-RAY DIFFRACTION98
2.9486-3.08270.33651270.2652522X-RAY DIFFRACTION97
3.0827-3.24520.32651310.2552506X-RAY DIFFRACTION97
3.2452-3.44850.28681400.2292500X-RAY DIFFRACTION97
3.4485-3.71460.26771670.21832478X-RAY DIFFRACTION97
3.7146-4.08820.24351520.22062553X-RAY DIFFRACTION99
4.0882-4.67920.20521340.19712543X-RAY DIFFRACTION98
4.6792-5.89310.18961490.19042496X-RAY DIFFRACTION97
5.8931-44.23030.21331170.2042563X-RAY DIFFRACTION98
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)
11.63540.38150.13741.8121-0.16762.1031-0.10010.24330.11270.0130.0943-0.0375-0.09010.328400.3425-0.03650.0030.46260.08210.4539-25.1958-4.3651125.1856
21.64730.21630.35032.00040.38711.33620.1263-0.1404-0.06720.4711-0.28250.31390.147-0.14990.00010.4474-0.04360.050.37180.01270.3809-21.83734.4239155.4806
31.4930.3127-0.23061.2549-0.02181.9834-0.01690.198-0.0229-0.07040.0633-0.02490.0018-0.3044-00.3491-0.0455-0.01060.4277-0.0920.3611-3.692428.6562125.2701
42.36741.4478-0.23042.6631-0.14621.42630.2537-0.34050.00160.5595-0.367-0.3622-0.10570.1568-0.00050.4412-0.041-0.03330.42560.03540.3775-7.001119.9017155.5278
50.01240.06320.01620.4853-0.01620.21190.0825-0.0303-0.0150.0227-0.0313-0.0202-0.0191-0.0705-00.35660.00350.01210.2427-0.0050.2464-13.646113.2429135.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 237:340 )A237 - 340
2X-RAY DIFFRACTION2( CHAIN A AND RESID 341:441 ) OR ( CHAIN E AND RESID 1:13 )A341 - 441
3X-RAY DIFFRACTION2( CHAIN A AND RESID 341:441 ) OR ( CHAIN E AND RESID 1:13 )E1 - 13
4X-RAY DIFFRACTION3( CHAIN B AND RESID 237:340 )B237 - 340
5X-RAY DIFFRACTION4( CHAIN B AND RESID 341:441 ) OR ( CHAIN F AND RESID 1:13 )B341 - 441
6X-RAY DIFFRACTION4( CHAIN B AND RESID 341:441 ) OR ( CHAIN F AND RESID 1:13 )F1 - 13
7X-RAY DIFFRACTION5( CHAIN A AND RESID 601:677 ) OR ( CHAIN B AND RESID 601:689 ) OR ( CHAIN E AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:103 )A601 - 677
8X-RAY DIFFRACTION5( CHAIN A AND RESID 601:677 ) OR ( CHAIN B AND RESID 601:689 ) OR ( CHAIN E AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:103 )B601 - 689
9X-RAY DIFFRACTION5( CHAIN A AND RESID 601:677 ) OR ( CHAIN B AND RESID 601:689 ) OR ( CHAIN E AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:103 )E101
10X-RAY DIFFRACTION5( CHAIN A AND RESID 601:677 ) OR ( CHAIN B AND RESID 601:689 ) OR ( CHAIN E AND RESID 101:101 ) OR ( CHAIN F AND RESID 101:103 )F101 - 103

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