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- PDB-2oqj: Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1 -

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Basic information

Entry
Database: PDB / ID: 2oqj
TitleCrystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
Components
  • Fab 2G12 heavy chain
  • Fab 2G12 light chain
  • peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Ig-like domain-containing protein / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCalarese, D.A. / Stanfield, R.L. / Menendez, A. / Scott, J.K. / Wilson, I.A.
CitationJournal: Faseb J. / Year: 2008
Title: A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120.
Authors: Menendez, A. / Calarese, D.A. / Stanfield, R.L. / Chow, K.C. / Scanlan, C.N. / Kunert, R. / Katinger, H. / Burton, D.R. / Wilson, I.A. / Scott, J.K.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 2G12 light chain
B: Fab 2G12 heavy chain
C: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
D: Fab 2G12 light chain
E: Fab 2G12 heavy chain
F: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
G: Fab 2G12 light chain
H: Fab 2G12 heavy chain
I: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
J: Fab 2G12 light chain
K: Fab 2G12 heavy chain
L: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)


Theoretical massNumber of molelcules
Total (without water)195,97612
Polymers195,97612
Non-polymers00
Water0
1
A: Fab 2G12 light chain
B: Fab 2G12 heavy chain
C: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
D: Fab 2G12 light chain
E: Fab 2G12 heavy chain
F: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)


Theoretical massNumber of molelcules
Total (without water)97,9886
Polymers97,9886
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-72 kcal/mol
Surface area40210 Å2
MethodPISA
2
G: Fab 2G12 light chain
H: Fab 2G12 heavy chain
I: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)
J: Fab 2G12 light chain
K: Fab 2G12 heavy chain
L: peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)


Theoretical massNumber of molelcules
Total (without water)97,9886
Polymers97,9886
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-67 kcal/mol
Surface area39770 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25760 Å2
ΔGint-146.8 kcal/mol
Surface area77890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.264, 171.348, 119.568
Angle α, β, γ (deg.)90.00, 105.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLYAA2 - 2121 - 211
21VALVALGLYGLYDD2 - 2121 - 211
31VALVALGLYGLYGG2 - 2121 - 211
41VALVALGLYGLYJJ2 - 2121 - 211
12GLUGLULYSLYSBB1 - 2281 - 224
22GLUGLULYSLYSEE1 - 2281 - 224
32GLUGLULYSLYSHH1 - 2281 - 224
42GLUGLULYSLYSKK1 - 2281 - 224

NCS ensembles :
ID
1
2
DetailsDimeric Fab 2G12-peptide complex, chains A, B, D, E (dimeric Fab) and C, F (peptides) / Dimeric Fab 2G12-peptide complex, chains G, H, J, K (dimeric Fab) and I, L (peptides)

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Components

#1: Antibody
Fab 2G12 light chain


Mass: 23001.648 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Fab 2G12 light chain / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PIH4
#2: Antibody
Fab 2G12 heavy chain


Mass: 23845.791 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Fab 2G12 heavy chain / Source: (natural) Homo sapiens (human) / References: UniProt: Q6N089
#3: Protein/peptide
peptide 2G12.1 (ACPPSHVLDMRSGTCLAAEGK)


Mass: 2146.491 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: synthetic peptide derived from a phage-displayed peptide library

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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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.33M Na/K phosphate, 0.2M isopropanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.7 Å / Num. all: 62018 / Num. obs: 62018 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 58.9 Å2 / Rsym value: 0.115 / Net I/σ(I): 9.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3095 / Rsym value: 0.476 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1op3 with carbohydrate removed from the Fab binding site

1op3
PDB Unreleased entry


Resolution: 2.8→48.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 39.562 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.23 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27461 3138 5.1 %RANDOM
Rwork0.23396 ---
all0.236 58837 --
obs0.236 58837 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.115 Å2
Baniso -1Baniso -2Baniso -3
1-9.14 Å20 Å27.85 Å2
2---5.87 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13685 0 0 0 13685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214020
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.95219074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26651803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12523.84526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.499152244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2711564
X-RAY DIFFRACTIONr_chiral_restr0.0650.22178
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210464
X-RAY DIFFRACTIONr_nbd_refined0.1790.24996
X-RAY DIFFRACTIONr_nbtor_refined0.2950.29399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2405
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.211
X-RAY DIFFRACTIONr_mcbond_it0.1561.59177
X-RAY DIFFRACTIONr_mcangle_it0.272214583
X-RAY DIFFRACTIONr_scbond_it0.40935477
X-RAY DIFFRACTIONr_scangle_it0.6774.54491
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1618medium positional0.290.5
12D1618medium positional0.350.5
13G1618medium positional0.340.5
14J1618medium positional0.310.5
21B1675medium positional0.280.5
22E1675medium positional0.290.5
23H1675medium positional0.320.5
24K1675medium positional0.280.5
11A1618medium thermal0.122
12D1618medium thermal0.142
13G1618medium thermal0.152
14J1618medium thermal0.122
21B1675medium thermal0.132
22E1675medium thermal0.132
23H1675medium thermal0.152
24K1675medium thermal0.132
LS refinement shellResolution: 2.8→2.898 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.525 300 -
Rwork0.443 5747 -
obs--97.99 %
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)
14.46221.2997-3.15127.9814-2.89974.18660.28240.34370.33230.09230.11280.7841-0.6607-0.3616-0.3951-0.29370.08770.0553-0.35160.0862-0.269943.468952.5558.0552
22.5822-3.4983-1.34549.4210.81583.0530.14480.3693-0.3378-1.0238-0.3760.03940.35840.15140.23120.0737-0.05380.0505-0.20910.0305-0.274864.9142.5266-17.1995
33.1622-0.3568-0.57716.074-0.50394.37540.01290.05660.04730.12920.070.2812-0.1071-0.0676-0.083-0.38530.00290.0439-0.4480.0583-0.391748.592932.307813.3661
43.6871-1.7283-1.012411.69621.5663.23850.55091.0740.033-1.7003-0.46770.064-0.0006-0.1433-0.08330.42960.2183-0.08110.0836-0.0758-0.272971.61163.0662-13.9216
52.4906-1.8409-0.56323.85760.10783.3706-0.3493-0.143-0.69980.25010.16430.35360.24140.16880.185-0.29380.07630.1453-0.39430.0512-0.25165.2052-7.264622.4123
61.28080.2258-0.731810.5915-4.63823.05020.21710.38210.4515-0.684-0.296-1.3226-0.20310.3210.0789-0.02640.03680.2482-0.1423-0.00610.062584.32374.213-4.2112
74.9089-0.7615-1.11025.5285-0.30863.4767-0.05020.0417-0.12220.2850.05670.231-0.05910.0485-0.0065-0.3720.03010.0679-0.48160.001-0.41658.082912.773319.7815
82.87620.0444-0.436710.277-1.52113.50270.09240.14860.3108-0.3118-0.5665-1.36130.09040.86310.4741-0.1339-0.0070.081-0.02530.18030.123677.473444.03-7.5103
93.29250.4842-1.5333.5483-0.54054.2706-0.2756-0.0524-0.8444-0.011-0.033-0.09090.2716-0.02570.3086-0.36040.01870.1056-0.443-0.0001-0.243421.9821-10.629734.3794
102.0689-1.0961-2.147.65042.76124.02610.1018-0.3454-0.07710.0981-0.1860.3823-0.2826-0.01170.0842-0.1619-0.0540.0686-0.20830.094-0.3121-0.7746-0.049158.5769
113.1758-0.1383-0.96194.85541.53574.2531-0.1178-0.1181-0.2387-0.0276-0.0024-0.23750.1252-0.04560.1202-0.3992-0.03130.0359-0.44940.0201-0.393527.78579.768438.2311
124.3027-1.4388-0.728111.60022.58435.72280.07590.04680.38820.1982-0.52482.0417-0.2282-1.13980.4489-0.1832-0.00590.0174-0.0778-0.20930.30094.012539.435264.2648
135.5273-0.6822-3.46977.10433.29214.74260.6486-0.43740.66590.03510.1936-0.8749-0.88320.499-0.8422-0.2586-0.17270.1436-0.2565-0.2534-0.035839.308549.478153.0447
143.03572.559-1.628112.02850.44472.33210.3739-0.54550.11041.5384-0.2450.32630.2659-0.0379-0.12890.0617-0.08760.0162-0.1407-0.1592-0.32415.440638.028675.3444
153.8255-0.0053-1.4215.64571.07135.06050.0769-0.22540.0768-0.13560.0175-0.4693-0.07840.1759-0.0944-0.4016-0.04620.0434-0.3805-0.1113-0.346235.454529.428246.4088
163.38361.5928-1.04659.4271-0.49364.06460.5888-0.9264-0.13531.3337-0.44870.0521-0.02530.2145-0.14010.1793-0.056-0.07530.08290.1822-0.322310.5405-1.302169.6499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1071 - 106
2X-RAY DIFFRACTION2AA108 - 212107 - 211
3X-RAY DIFFRACTION3BB1 - 1131 - 123
4X-RAY DIFFRACTION4BB114 - 228124 - 224
5X-RAY DIFFRACTION5DD2 - 1071 - 106
6X-RAY DIFFRACTION6DD108 - 212107 - 211
7X-RAY DIFFRACTION7EE1 - 1131 - 123
8X-RAY DIFFRACTION8EE114 - 228124 - 224
9X-RAY DIFFRACTION9GG2 - 1071 - 106
10X-RAY DIFFRACTION10GG108 - 212107 - 211
11X-RAY DIFFRACTION11HH1 - 1131 - 123
12X-RAY DIFFRACTION12HH114 - 228124 - 224
13X-RAY DIFFRACTION13JJ2 - 1071 - 106
14X-RAY DIFFRACTION14JJ108 - 212107 - 211
15X-RAY DIFFRACTION15KK1 - 1131 - 123
16X-RAY DIFFRACTION16KK114 - 228124 - 224

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