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- PDB-2x7l: Implications of the HIV-1 Rev dimer structure at 3.2A resolution ... -

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Basic information

Entry
Database: PDB / ID: 2x7l
TitleImplications of the HIV-1 Rev dimer structure at 3.2A resolution for multimeric binding to the Rev response element
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
  • PROTEIN REV
KeywordsIMMUNE SYSTEM / NUCLEAR EXPORT / POST-TRANSCRIPTIONAL REGULATION
Function / homology
Function and homology information


host cell nucleolus / viral process / mRNA transport / protein export from nucleus / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding
Similarity search - Function
Helix Hairpins - #630 / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Helix Hairpins / Helix non-globular / Special / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsDiMattia, M.A. / Watts, N.R. / Stahl, S.J. / Rader, C. / Wingfield, P.T. / Stuart, D.I. / Steven, A.C. / Grimes, J.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Implications of the HIV-1 Rev Dimer Structure at 3. 2 A Resolution for Multimeric Binding to the Rev Response Element.
Authors: Dimattia, M.A. / Watts, N.R. / Stahl, S.J. / Rader, C. / Wingfield, P.T. / Stuart, D.I. / Steven, A.C. / Grimes, J.M.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Generation and Characterization of a Chimeric Rabbit/Human Fab for Co-Crystallization of HIV-1 Rev.
Authors: Stahl, S.J. / Watts, N.R. / Rader, C. / Dimattia, M.A. / Mage, R.G. / Palmer, I. / Kaufman, J.D. / Grimes, J.M. / Stuart, D.I. / Steven, A.C. / Wingfield, P.T.
History
DepositionMar 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Feb 20, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 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: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
C: FAB HEAVY CHAIN
D: FAB LIGHT CHAIN
E: FAB HEAVY CHAIN
F: FAB LIGHT CHAIN
G: FAB HEAVY CHAIN
H: FAB HEAVY CHAIN
I: FAB LIGHT CHAIN
J: FAB HEAVY CHAIN
K: FAB LIGHT CHAIN
L: FAB LIGHT CHAIN
M: PROTEIN REV
N: PROTEIN REV
O: PROTEIN REV
P: PROTEIN REV
Q: PROTEIN REV
R: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)365,00318
Polymers365,00318
Non-polymers00
Water00
1
E: FAB HEAVY CHAIN
F: FAB LIGHT CHAIN
R: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-47.8 kcal/mol
Surface area27060 Å2
MethodPQS
2
C: FAB HEAVY CHAIN
D: FAB LIGHT CHAIN
P: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-47.3 kcal/mol
Surface area27030 Å2
MethodPQS
3
G: FAB HEAVY CHAIN
I: FAB LIGHT CHAIN
M: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-47.8 kcal/mol
Surface area26970 Å2
MethodPQS
4
J: FAB HEAVY CHAIN
K: FAB LIGHT CHAIN
Q: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-47.4 kcal/mol
Surface area27020 Å2
MethodPQS
5
H: FAB HEAVY CHAIN
L: FAB LIGHT CHAIN
N: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-47.7 kcal/mol
Surface area27030 Å2
MethodPQS
6
A: FAB HEAVY CHAIN
B: FAB LIGHT CHAIN
O: PROTEIN REV


Theoretical massNumber of molelcules
Total (without water)60,8343
Polymers60,8343
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-48.4 kcal/mol
Surface area27080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)87.678, 87.692, 176.334
Angle α, β, γ (deg.)94.86, 95.50, 104.60
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
FAB HEAVY CHAIN


Mass: 24492.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUSRIL
#2: Antibody
FAB LIGHT CHAIN


Mass: 23416.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUSRIL
#3: Protein
PROTEIN REV / ART/TRS / ANTI-REPRESSION TRANSACTIVATOR / REGULATOR OF EXPRESSION OF VIRAL PROTEINS


Mass: 12924.489 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUSRIL / References: UniProt: P04616
Has protein modificationY
Sequence detailsTHE C-TERMINAL DOMAIN OF REV IS DISORDERED IN THE CRYSTAL STRUCTURE. N-TERMINAL MET HAS BEEN ...THE C-TERMINAL DOMAIN OF REV IS DISORDERED IN THE CRYSTAL STRUCTURE. N-TERMINAL MET HAS BEEN CLEAVED OFF IN E. COLI AUTHOR PROVIDED GENBANK ACCESSION NUMBERS: CHAINS A,C,E,G,H,J GU223202 CHAINS B,D,F,I,K,L GU223201 CHAINS M,N,O,P,Q,R AAL29461

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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: 4.11 Å3/Da / Density % sol: 69.83 %
Description: 18 DIFFERENT MODELS USED IN PHASER AS AN ENSEMBLE
Crystal growpH: 8.5
Details: 12% POLYETHYLENE GLYCOL (PEG) 6000, 100 MM DI-AMMONIUM PHOSPHATE (DAP), AND 100 MM TRIS/HCL (PH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→48.8 Å / Num. obs: 83664 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 77.96 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85

1jps

2qr0

2r8s

3bdy

1tzh

1za3

2r0k

2v7n

3dvg

1b2w

1bey

1tzi

2fjf

2qqn

1b4j

2fgw

2fjh

3d85


Resolution: 3.17→48.78 Å / Cor.coef. Fo:Fc: 0.8909 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4187 5.01 %RANDOM
Rwork0.2337 ---
obs0.2346 83636 --
Displacement parametersBiso mean: 143.62 Å2
Baniso -1Baniso -2Baniso -3
1--18.228 Å213.1177 Å2-6.3827 Å2
2---15.9372 Å2-4.1363 Å2
3---34.1652 Å2
Refine analyzeLuzzati coordinate error obs: 1.029 Å
Refinement stepCycle: LAST / Resolution: 3.17→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22554 0 0 0 22554
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123112HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3231500HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7632SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes468HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3378HARMONIC5
X-RAY DIFFRACTIONt_it23112HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion23.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3102SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25991SEMIHARMONIC4
LS refinement shellResolution: 3.17→3.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2881 274 4.95 %
Rwork0.2777 5261 -
all0.2782 5535 -
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)
15.91580.04770.59166.8328-0.49649.63310.0923-1.27610.70960.3069-0.0723-0.8380.22951.0624-0.01990.67430.00050.0076-0.42830.071-0.51732.7648-0.197686.3652
21.15490.43350.08852.58170.90644.8127-0.0971-0.06120.09840.17530.1702-0.05690.19070.0117-0.07310.69310.0438-0.0254-0.68550.011-0.299734.3512-26.191341.5481
314.23824.866-1.462512.17670.7738.424-0.02180.96380.4171-0.35840.0507-1.0680.57221.4061-0.02890.7217-0.1240.0275-0.10620.0999-0.596148.7523-23.82465.7872
40.91880.3054-0.01553.7436-1.15584.5393-0.2384-0.0185-0.06160.16980.41290.14150.3271-0.361-0.17450.67960.03740.0467-0.6821-0.0011-0.354838.9756-42.707945.3623
56.54630.95590.15487.1662-0.63013.56230.0359-0.39930.37540.17450.0911.0642-0.9036-0.7306-0.12690.1182-0.34180.05060.4739-0.0238-0.5659-22.7754-31.107482.4664
62.99922.03890.32054.0363-0.6118.1101-0.09390.39130.2908-0.98980.04780.0449-0.54510.45440.04610.2952-0.22360.1019-0.17690.0752-0.3612-6.9363-26.06347.2141
76.6693-0.4252-0.25456.5831.45938.7290.2440.5656-1.0402-1.14120.00960.05021.01590.2241-0.2536-0.1904-0.3140.02220.44290.0522-0.4364-9.1771-54.373988.32
82.43871.2525-0.19462.79211.37134.451-0.22320.2531-0.3464-1.25140.192-0.3362-0.18531.17610.03120.6162-0.11380.2961-0.2491-0.0058-0.5389-10.2274-41.798240.4657
97.83332.45221.564616.3961-0.92684.3412-0.0691-0.6668-1.31610.7780.27510.62771.08090.5975-0.2060.0442-0.38630.18270.44720.0177-0.579817.9219-64.7313168.9562
102.6170.0690.3440.67890.31183.85260.15090.262-0.09890.0776-0.17780.07860.1708-0.01460.0269-0.4466-0.45050.02550.4807-0.1802-0.301416.4529-49.6849133.1572
113.51750.4651-1.35981.10490.01153.91810.2370.45740.27280.0084-0.09990.022-0.42110.3786-0.1371-0.4649-0.403-0.03750.4783-0.0272-0.324633.5699-49.9481129.3281
121.70060.9929-0.01054.0970.18378.83250.1489-0.823-0.05580.3519-0.27230.38990.9019-0.88370.1234-0.1563-0.47110.06450.21420.0849-0.51325.7662-9.5231127.452
131.1612-0.2836-0.53242.21030.10197.67990.0578-0.0454-0.1226-0.54120.0109-0.27330.0410.0201-0.06870.6550.1282-0.0745-0.6391-0.0015-0.037727.6102-3.412147.9094
141.0253-0.04520.54212.326-0.96743.38450.3336-0.9351-0.10490.1532-0.3452-0.30481.14750.02710.0116-0.056-0.413-0.0680.39170.1523-0.557320.125-2.3292134.217
152.7913-0.10940.42211.4138-0.79296.24420.0978-0.4454-0.15190.04560.0617-0.1846-0.0520.1863-0.1595-0.5834-0.18050.00870.424-0.1759-0.0539-7.3501-48.7364126.7643
162.8194-0.2679-0.96620.3792-0.20917.02590.102-0.68440.11840.10930.0764-0.0998-0.4447-0.0552-0.1784-0.6004-0.1612-0.02250.6317-0.1309-0.1904-24.4142-49.928130.5796
171.0308-0.9758-0.12693.0835-0.53936.04420.14120.0951-0.058-0.59540.04950.0828-0.4143-0.5462-0.19060.63910.1562-0.062-0.618-0.0191-0.168524.51913.400544.119
186.8838-0.68380.23868.2266-0.39173.43970.26290.2120.7679-0.5329-0.08950.5459-0.3599-1.1952-0.17350.6226-0.1685-0.01320.01390.0003-0.57716.72457.155192.1848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN N)
2X-RAY DIFFRACTION2(CHAIN A)
3X-RAY DIFFRACTION3(CHAIN O)
4X-RAY DIFFRACTION4(CHAIN B)
5X-RAY DIFFRACTION5(CHAIN P)
6X-RAY DIFFRACTION6(CHAIN C)
7X-RAY DIFFRACTION7(CHAIN Q)
8X-RAY DIFFRACTION8(CHAIN D)
9X-RAY DIFFRACTION9(CHAIN R)
10X-RAY DIFFRACTION10(CHAIN E)
11X-RAY DIFFRACTION11(CHAIN F)
12X-RAY DIFFRACTION12(CHAIN G)
13X-RAY DIFFRACTION13(CHAIN H)
14X-RAY DIFFRACTION14(CHAIN I)
15X-RAY DIFFRACTION15(CHAIN J)
16X-RAY DIFFRACTION16(CHAIN K)
17X-RAY DIFFRACTION17(CHAIN L)
18X-RAY DIFFRACTION18(CHAIN M)

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